This is actually a different bug, completely unrelated to what happened to items in some Guild Banks.
On the bright side, those items are not actually gone but simply not visible. That said, a fix is being worked on to make sure they appear again 
Guild banks are “fixed”.
To the best of our knowledge, the problem that caused items from guild banks to disappear was found and sorted a few days ago; it should be safe now to use guild banks again.