Guild bank items disappear
Best bet is to file a ticket.
Sorrow’s Furnace US
This happens sometimes, where depositing or withdrawing things from the Guild Bank disappear. They usually show back up within a few hours to a day or so. Even though the slot you put them in appears blank, you can not put anything else there, as they are actually there, just invisible.
Sometimes, just re-logging helps. Good luck. =)