Hi
Here are instructions for doing an Upgrade of Windows 10 from Windows 10.
It says that this will maintain all your files and software just as a upgrade from Windows 7 or 8 would.
Repair Install Windows 10 with an In-place Upgrade
What I would recommend is take the time to create a System Backup, using software like EaseUS Backup and create the bootable repair disk that it will make for you.
My system is like yours with Windows on a drive of it's own, it takes me about 20 minutes to make or restore a backup.
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This is what I use, you can use any backup software that you want, save the backup on your second hard drive.
Then go ahead and do the in place upgrade.
If it doesn't do what you want, you can use...