Currently it is possible to lose the item you deposit into guild bank completely. I have been taking crafted food from guild bank for writs but I have noticed that sometimes the food I deposit back to the bank is gone. I checked the bank log of all my guilds and there is no deposit entry for the food I have taken. I also checked all my characters to make sure the food is not in my inventory as well as my personal bank. Nope, its gone. It has happened several times and it looks like it has something to do with closing the guild bank interface before the actual deposit transaction is done.