I’m quite a bit hopeful given the answer I got on another thread… Guild banks - #22 by Agrias-bloodsail-buccaneers
There’s a chance everything is still there and they will just need to fix the issue so the items are “visible” again.
Update: 8/25
Unfortunately I just found another slot “go empty” in my warbank. I’ve been trying to avoid doing things like sorting my bank, my warbank, etc. It would be nice to get an update on the guild bank, war bank, item “missing” issue.