Thanks for looking into those things. That’s good to know it’s probably not involved with travel or odd work time combinations. Such things can be a bit of a pain to test for! While we could have speculated that the bug didn’t manifest until you finally closed it (this file is not written during routine auto-saves, only on manual saves and shutdown), the fact that the routine project backups were okay does mean the copy held in memory was okay, too, until recently.
Unfortunately that doesn’t leave me with a whole lot to check against though!
I presume there is nothing unusual that happened around that time, no system updates applied? As for Scrivener, the last update was in December, so nothing has changed with the code since then. You can’t rule out system updates though, as they can have extremely specific impacts on Mac software (like this one, that popped up out of the blue several weeks ago).
At least you do have a very recent copy of that file that is correct. It is perfectly safe to transpose that copy (perhaps with the last line or two copied from the current version) into your project while it is closed. It is entirely self-contained.