I have Firefox set to ask me where to save downloads, so it stores last save folders on a per-site basis. It also appears to store upload folders on a per-site basis. I don't know whether it does this with the base configuration of saving automatically rather than prompting where to save.

Note: private windows do not save this information to disk.

If you notice Firefox using per-site logic for uploads, but no longer updating that after each upload, there might be a problem with the database file Firefox uses to store this information, content-prefs.sqlite. This file also stores your per-site zoom levels, so if those aren't saved either, I would definitely suspect a file problem.

Thank you so much. This was very helpful. And you telling me the folder name causing the issue helped me find this question of someone having a similar problem and the "chosen solution" then gave me exactly the answer I was looking for: https://support.mozilla.org/bm/questions/1423091

It's now been resolved. Once again, thank you for your help.