Windows Server Essentials re-install best practice

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samsquared2

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Once again, I need to re-install WSE 2016. I have the OS installed in a 120GB partition using the original drives (no reformatting, drive wiping, etc. from the previous setup), but don't know how to proceed from here. I have 2 SSDs attached now:

SSD1 - 1TB Disk 0 which currently contains the 120GB C: drive and another 813.83GB partition listed as "Healthy (Storage Spaces Protective Partition).
SSD2 - 1TB Disk 2 showing as offline with a space of 1740.87. This and the first drive were part of a storage pool

I also have another 1TB drive which I'd like to attach externally for additional storage but it seems a better idea to get what I have working before adding that to the mix.

Can I make what I have work or should I format SSD1 and 2 and start over?

 
Last edited by a moderator:
Yes — you can make this work, but the cleanest path is to wipe the old Storage Spaces metadata from SSD1 and SSD2 first and then rebuild the backup storage from scratch.
Right now both disks still contain remnants of the old Storage Spaces pool:
  • SSD1 has an 813.83 GB Storage Spaces Protective Partition
  • SSD2 shows a strange 1740.87 GB offline size, which is classic leftover pooled-disk metadata behavior
That means Windows is still seeing parts of the old virtual disk/pool, not two normal 1 TB SSDs.

My recommendation​

Best practice​

  1. Keep the current OS install on C: if it's already good.
  2. Delete the old Storage Spaces remnants on both SSDs.
  3. Rebuild your backup storage cleanly using:
    • the free space on SSD1
    • all of SSD2
  4. Only after that, attach the external 1 TB drive.

Important warning​

If there is any data left in the old storage pool that you still need, stop before wiping anything.
If not, then wiping the old pool metadata is the right move.

What I would do​

Option A — Recommended​

  • Keep the 120 GB C: partition
  • Wipe only:
    • the 813.83 GB Storage Spaces Protective Partition on Disk 0
    • all old metadata on Disk 2
  • Then create a new single backup target
This is the least disruptive option.

Option B — Full clean restart​

  • Wipe both SSDs completely
  • Reinstall WSE 2016 from scratch
  • Recreate OS + backup storage from zero
This is cleaner conceptually, but unnecessary if your current OS install is stable.

GUI-first plan​

Step 1: Make sure the OS install is healthy​

Before touching storage:
  1. Boot the server normally.
  2. Confirm:
    • C: is stable
    • Dashboard opens
    • networking works
    • Windows Updates/install status is normal
  3. If all of that is fine, proceed.
If the OS itself is questionable, then go to Option B and start over fully.

Step 2: Remove the old Storage Spaces parts​

Because Disk Management is not good at clearing old pooled disks, use PowerShell or DiskPart.

Safer approach​

You want to clear only the non-OS areas.

For Disk 0​

You must not wipe the whole disk, because it contains:
  • System Reserved
  • C:
You only want to remove the old Storage Spaces partition.

For Disk 2​

You can usually wipe the whole disk.

Step 3: Clean Disk 2 completely​

Open Command Prompt as Administrator and run:
Code: 
diskpart
list disk
select disk 2
attributes disk clear readonly
online disk
clean
convert gpt
exit

Expected result​

  • Disk 2 becomes a normal empty 1 TB disk
  • In Disk Management it should show as Unallocated
  • It should no longer show the weird 1740.87 GB value

Step 4: Remove the protective partition from Disk 0​

Because Disk 0 contains the OS, be careful.
In Admin Command Prompt:
Code: 
diskpart
list disk
select disk 0
list partition
Identify the large 813.83 GB partition.
Then:
Code: 
select partition <number>
delete partition override
exit

Expected result​

  • Disk 0 keeps:
    • System Reserved
    • C:
  • The 813.83 GB area becomes Unallocated
Do not delete the wrong partition.

Step 5: Decide how to use the space​

You then have two reasonable choices.

Choice 1 — Simple and recommended​

Use Disk 2 only for client backups.
Why:
  • Keeps OS disk and backup disk separate
  • Easier recovery later
  • Fewer Storage Spaces complications

Choice 2 — Larger pool​

Use:
  • free space on Disk 0
  • all of Disk 2
This gives more total backup space, but it mixes OS and backup storage on the same physical disk, which is less ideal.
For a home WSE setup, I would strongly favor:
  • Disk 0 = OS only
  • Disk 2 = backups only
  • External 1 TB = extra storage or secondary backup

Step 6: If you want the cleanest layout​

After deleting the 813.83 GB partition on Disk 0, I would actually leave it unused for now unless you truly need it.
That gives you:
  • Disk 0
    • System Reserved
    • C:
    • unused space
  • Disk 2
    • dedicated backup target
This is much simpler than rebuilding a two-disk Storage Space.

My practical recommendation​

Given your history with this server, I would do this:
  1. Keep current C: install
  2. Delete old Storage Spaces partition from Disk 0
  3. Fully clean Disk 2
  4. Use Disk 2 alone for Client Computer Backups
  5. Later attach the external 1 TB drive for:
    • server folders
    • exported backups
    • secondary copy of critical files
That avoids repeating the exact Storage Spaces confusion you've already hit multiple times.

When I would start over completely​

I would only wipe both SSDs and reinstall from zero if:
  • the current WSE install is unstable
  • Dashboard/services are broken
  • connector install is failing
  • backup configuration is badly corrupted
  • you want a completely clean long-term setup
If the OS is working now, I would not reformat SSD1 fully.

One correction to note​

Your screenshot shows Disk 2 as offline and 1740.87 GB, which strongly suggests the system still sees pooled metadata, not a normal disk. That is not something I would try to "reuse as-is." It should be cleaned first.

Bottom line​

No, you do not need to wipe everything and start over.
Yes, you should clear the old Storage Spaces data from both disks before proceeding.

Best path:​

  1. Keep C:
  2. Delete the protective partition on Disk 0
  3. Clean Disk 2 fully
  4. Use Disk 2 as your backup disk
  5. Add the external drive only after the server is stable
If you want, I can give you a very careful exact step-by-step for:
  • identifying the correct partition number on Disk 0
  • cleaning Disk 2 safely
  • then setting up client backups in WSE 2016 using GUI only.
 
I think I need to redo the install from scratch. Even though the OS appears to be fine and is receiving Windows updates:

1. The install did not ask me where to place the OS or what size the partition size should be.​
2. The Windows Server Essentials Email service is disabled which is the state I put it in after the previous install because it wouldn't start (WSE Email service won't start)​
​
Pease send instructions for starting from scratch.​
 
If you want a truly clean rebuild, I agree: start from scratch.
Because you’ve had repeated Storage Spaces remnants and the old disabled Email service carried forward, a full wipe is the best way to avoid dragging old configuration back in.

Before you begin​

Back up anything you need​

  1. Copy off any files you want to keep from the server.
  2. Make sure you have:
    • your WSE 2016 install media
    • product key
    • network settings if you use a static IP
    • any notes about users, shares, and backup settings

Disconnect anything not needed​

For the cleanest install:
  1. Leave connected only:
    • SSD1
    • keyboard/mouse/monitor
    • network
  2. Disconnect SSD2
  3. Do not attach the external 1 TB drive yet
This prevents Setup from putting boot files or Storage Spaces metadata on the wrong disk.

Clean install from scratch​

Part 1: Wipe SSD1 completely and install WSE 2016​

Step 1: Boot from the WSE 2016 installer​

  1. Boot from the Windows Server Essentials 2016 USB/DVD.
  2. Proceed until you reach the disk selection screen.

Step 2: Delete all partitions on SSD1​

At the screen asking Where do you want to install Windows?
  1. Select each partition on SSD1 / Disk 0
  2. Click Delete
  3. Repeat until the entire disk shows as Unallocated Space
You should delete:
  • System Reserved
  • old C:
  • old Storage Spaces partition
  • anything else on that disk

Step 3: Install to the unallocated disk​

  1. Select the unallocated space on SSD1.
  2. Click Next

Important note about partition size​

WSE/Windows Server setup may not ask you what size to make C: during install. That is normal if you install directly to unallocated space.
If you want a smaller OS partition, do this before clicking Next:
  1. Click New
  2. Enter the size you want for the OS partition
For a 120 GB C: partition, enter roughly:
122880
That value is in MB.
Setup will also create the small system partitions automatically.
If you do not do this, Windows will usually take the whole disk for the OS.

Step 4: Finish installation​

  1. Let Setup complete.
  2. Complete first boot configuration.
  3. Install all Windows Updates.
  4. Confirm the server is stable before reconnecting other drives.

Part 2: Prepare SSD2 after the OS is fully installed​

Only after the OS install is complete and working:
  1. Shut down the server.
  2. Reconnect SSD2
  3. Boot into Windows

Step 5: Clean SSD2 completely​

Open Command Prompt as Administrator and run:
Code: 
diskpart
list disk
select disk 1
clean
convert gpt
exit

Warning​

Make sure the disk number is actually SSD2 before using clean.
If you are unsure, stop and verify size carefully.

Part 3: Decide on storage layout​

My recommendation​

Keep it simple this time:
  • SSD1 = OS only
  • SSD2 = client backups
  • External 1 TB = extra storage later
That will be much easier to manage than mixing backup space into the OS disk.

Why this is better​

  • easier recovery
  • less Storage Spaces confusion
  • less risk of wiping the OS disk later
  • simpler troubleshooting

Part 4: Configure client backup storage​

Once SSD2 is clean and visible:
  1. Open Disk Management
  2. Confirm SSD2 appears as a normal unallocated 1 TB disk
  3. Let WSE use that disk for backup storage, or create a normal NTFS volume first depending on how you want to manage it
If you want the simplest route, I’d use it as a plain backup target rather than trying to recreate a more complex pooled setup immediately.

Part 5: About the Email service​

Since that was broken in the previous install, I would strongly suggest:
  1. Do not spend time on email during initial install
  2. Get these working first:
    • OS
    • Dashboard
    • users
    • shares
    • client connector
    • client backups
  3. Only after the server is stable, revisit outbound email
That way, if email breaks again, you know the base install is still good.

Recommended install order​

  1. Install WSE 2016 cleanly on SSD1 only
  2. Run Windows Update fully
  3. Confirm Dashboard works
  4. Create users/shares
  5. Reconnect and clean SSD2
  6. Configure backup storage
  7. Test one client backup
  8. Add external 1 TB later
  9. Revisit email last

One important detail​

You said the previous install did not ask where to place the OS or what size the partition should be.
That usually means one of these happened:
  • you used an automated/Essentials flow that accepted defaults
  • the disk still had existing partitions and Setup reused them
  • you didn’t manually click New on unallocated space
For a true clean rebuild, the key is:
  • delete every partition on SSD1
  • then create the OS partition size manually before continuing

Exact summary​

What to disconnect​

  • SSD2
  • external 1 TB drive

What to wipe​

  • all partitions on SSD1 during Setup
  • all of SSD2 after install

What to build​

  • SSD1: fresh OS install
  • SSD2: backup storage only
If you want, I can next give you:
  1. a very short checklist to print and follow during install, or
  2. the exact post-install steps for cleaning SSD2 and setting up client backups.
 
The first install went to SSD1 (SATA 0) and because it did not ask where to place the install, I think that I should put SSD2 on SATA 0 to keep that from happening again. What do you think?
 
I would not swap SSD2 onto SATA 0 just to force the installer.
The better fix is simpler:

Recommendation​

  1. Leave only the target install drive connected
  2. Boot from the installer
  3. At the Where do you want to install Windows? screen:
    • delete all partitions on that one SSD
    • create the partition size you want
    • install there
If only one internal SSD is attached, Windows Setup has no real choice but to use that disk.

Why I would avoid swapping ports unless necessary​

  • SATA port number by itself is not the real problem
  • The real problem is usually:
    • multiple disks attached during install
    • leftover partitions/metadata
    • clicking through setup defaults too quickly
  • Moving drives around can add confusion later when you’re trying to identify disks

Best practice for your reinstall​

Before installing​

  1. Disconnect SSD2
  2. Disconnect the external 1 TB
  3. Leave connected only:
    • SSD1 on its current port
    • installer USB/DVD
    • keyboard/mouse/monitor/network

During setup​

  1. When you reach disk selection, confirm there is only one disk
  2. Delete all partitions on that disk
  3. Click New
  4. Enter the size for the OS partition if you want C: limited to about 120 GB
  5. Select that new partition and install
If setup still skips the disk screen entirely, then that suggests:
  • you may be booting a preconfigured/unattended install source
  • or using an Essentials-specific install path that auto-partitions
In that case, changing SATA ports probably still won’t solve the root issue.

My answer​

  • No, I would not move SSD2 to SATA 0 just for this
  • Yes, I would disconnect every other storage device and install with only SSD1 attached

One exception​

If your BIOS/UEFI or motherboard clearly treats SATA 0 specially and you’ve seen odd behavior before, then moving the intended OS disk to SATA 0 is not harmful — but it should be treated as optional, not necessary.

Safest path​

  1. Keep SSD1 as the install target
  2. Disconnect all other drives
  3. Wipe SSD1 completely during setup
  4. Install
  5. Reconnect SSD2 only after Windows is fully installed
If you want, I can give you a minute-by-minute install checklist for the exact screens to watch for so you can avoid the automatic whole-disk install again.
 
I think I need to do something to SSD1 before continuing the install. I disconnected SSD2 but when the install gets to the point of selecting a disk, the options are

"Drive 0 Partition 1: System Reserved" and "Driven 0 Partition 2", which has a size of 117.2GB. If I remove that and try to create a new partition, the maximum size available is 120GB which is the size of the previous partition. I see no reason to proceed with the install.

Do I need to remove SSD1, attach it externally to another PC, and remove all partitions?
 
No — you do not need to remove SSD1 and attach it to another PC.
What you need is to wipe SSD1 completely from the Windows Setup screen so Setup sees the whole 1 TB as unallocated. Right now, Setup is only seeing the old 120 GB OS partition area, which means the rest of the disk is still tied up in old partition/storage metadata.

What should be happening​

On a clean 1 TB SSD, you should eventually see something like:
  • Drive 0 Unallocated Space
  • roughly 931 GB
Since you only see:
  • 500 MB System Reserved
  • 117.2 GB Primary
that means the old large partition is still not being exposed properly to Setup.

Best fix: use DiskPart from inside Setup​

Do this from the installer itself.

Step 1: Open Command Prompt in Setup​

At the disk selection screen, press:
Shift + F10
That opens a Command Prompt.

Step 2: Run DiskPart​

Type:
Code: 
diskpart
list disk
You should see your SSD as Disk 0 around 931 GB.

Step 3: Select the disk​

select disk 0

Step 4: Wipe the partition table completely​

clean
This removes all partitions and old metadata from SSD1.

Step 5: Convert to GPT​

Code: 
convert gpt
exit
exit

Step 6: Refresh Setup​

Back at the install screen:
  1. Click Refresh
  2. You should now see:
    • Drive 0 Unallocated Space
    • around 931 GB
If you do, you're back in business.

If you want a 120 GB OS partition​

Once the disk shows as all unallocated:
  1. Select the unallocated space
  2. Click New
  3. Enter:
122880
That is about 120 GB in MB.
Windows will create:
  • small system partitions
  • the main OS partition
Then install Windows to that partition.

Why this is better than using another PC​

  • faster
  • cleaner
  • same result
  • avoids USB enclosure issues
  • avoids accidentally initializing the disk differently on another machine

Important warning​

clean erases the disk layout completely.
That is exactly what you want here if you are truly reinstalling from scratch.

Double-check before running it​

Make sure:
  • SSD2 is disconnected
  • only the install target SSD is attached internally
  • list disk shows only the installer media and the 1 TB SSD
If you're unsure, stop at list disk and compare the sizes.

If clean still doesn’t fix it​

Very unlikely, but if after clean + Refresh the installer still only shows 120 GB:
  1. go back into DiskPart
  2. run:
Code: 
select disk 0
detail disk
list partition
If needed, I can help interpret that output.

Exact commands to use​

Code: 
diskpart
list disk
select disk 0
clean
convert gpt
exit
exit
Then click Refresh.

Expected result​

You should see approximately:
  • Drive 0 Unallocated Space
  • 931.5 GB
If you want, reply with what list disk shows before you run clean, and I’ll confirm you’re selecting the correct disk.
 
You’re running into leftover Storage Spaces metadata, which Disk Management won’t fully clean up on its own and that’s why things look weird. Before you wipe everything, try this: open PowerShell as admin and run Get-StoragePool. If the old pool still shows up, delete it from there using Remove-StoragePool. If it doesn’t, then use diskpart, run list disk, then select disk 2, then clean to fully strip that hidden config off SSD2. Do the same for the large protective partition on SSD1 if you want to reclaim it. Once both drives are clean, bring Disk 2 online and reinitialize it in Disk Management. That usually fixes the mismatch without needing a full OS reinstall and keeps your current C intact.
 
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