Well, chkdsk should run on an exFAT filesystem, especially if the dirty bit is set.
What happens exactly (what do you see) when you try to run CHKDSK on such a filesystem (from command line, running first just CHKDSK, and then CHKDSK /F)?
Which OS are you running?
You can manually flip the dirty bit, but it is senseless .
Just in case:
I don’t think turning off the dirty bit is safe, it is trying to tell you something, so it would be use at your own risk!!!
BTW: exFAT has the dirty bit in the VBR (1st Sector), offset 106. Since there are 4 flags in this single byte, you would need to change a bit, not a byte or nibble – or you would damage other flags located in this same offset. It is truley a dirty bit, not a dirty byte.
Offset 0 is Active FAT and indicates which FAT is active Offset 1 is Dirty Volume, 0=clean, 1=dirty Offset 2 is Media Failure, this indicates if there are ANY bad clusters on the volume Offset 3 is Clear to Zero (the spec does not indicate what this means)
Although the VBR has a checksum to prevent tampering, the flag bytes are not included in the checksum calculation.
It sounds like from your problem, chkdsk either can’t find the problem, or can’t fix the problem. So, if there is corruption in there, you probably won’t easily find it. This leaves you at a disadvantage because unless you locate and fix the corruption (if you can even find it) it will come back and haunt you someday.