Thanks to the logs and database of another user (who did not post on this thread), we’ve identified an issue. It may not be the only issue at play, but a preliminary fix does resolve this one user’s situation.
It’s not related to codepages, but that was a good guess. It is related to unicode normalization being different on different filesystems by default (good guess @Bill_Janssen!), and when copies were made, the normalization of file paths was changed.
We have the fix in internal testing now, and it’ll roll out in the next quick-fix release assuming all goes well.