Along the lines of DarkArvan.

It sounds like the local directory where the data is stored by default (C:\Users\<username>\Documents\My Games\Final Fantasy XIV may have gotten corrupted, possibly along with part of your user profile. Screenshots are by default saved here as well.

If you have OneDrive, then this directory would be synced and if MS had one of it's infamous hiccups then the data may have gotten borked. If this happened, since the cloud is 'never' the source of the issue, OneDrive will just resync the cloud copy back down to local. The OS can correct minor profile errors automatically as well as on startup, but if something got out of sync, of corrupted, then sadly you are back at square one.

If you have OneDrive I would definitely look into excluding the FF14 directory from the Sync, and once you get the settings back to where you want them, make a backup copy of the directory so you at least have a starting point should they be lost again.