When Windows claims "\WINDOWS\" is missing or corrupted

I have recently been trying to repair a Windows 10 machine that suddenly decided to stop booting, failing at startup with a message stating that a required file was missing or corrupted, with the error code 0xC000000D. What's strange is that it said \WINDOWS\ was the missing file. That directory is definitely there. None of these things helped:

• Startup Repair
• System Restore from a recovery environment (failed with an unspecified error)
• chkdsk (made corrections but didn't change the error)
• sfc offline
• dism offline
• Replacing the EFI files from a nearly-identical machine
• Recreating the BCD store

I am at a loss as to what to do here. Currently the best option seems to be a reinstall - all the data is safe and has been copied off.