I've got exactly this problem a while ago on my SSD Windows drive.
So if all of these commands don't work:
bootrec /fixboot
bootrec /fixmbr
bootrec /rebuildbcd
bootsect /nt60 sys /force
then there might be another problem with your system.
" Remove non-bootable discs (HDD, SSD...)
The first and easiest fix is to check for any existing media in your USB ports, or optical drives (CDs, DVDs).
BOOTMGR error will appear if your computer is trying to boot from one of these drives that have a non-bootable media inserted.
Consider changing the boot order from BIOS to make sure your PC boots from the hard drive and not from any other non-bootable."
In my case the problem was the second drive I had, a HDD unit full of bad sectors and possible other problems which surprisingly did affected the SSD Windows drive. I replaced the old HDD with a new one and problem is gone since then. No more missing files. I don't understand how and why a faulty HDD affects another SSD with Windows on it...
If you have other drives, try to disconnect all of them, keep only the system one, after that, run all the commands above and see if it works for you too.
It doesn't hurt to try.