I’m experiencing this bug also and I assume it’s because the items are marked as Unique (20). When you first go over the cap, the items in your warbank become invisible, but they’re still in the bank if you switch to another character. However, if you log back onto your first character without reducing the number in your warbank, the items in your character’s bags are deleted it seems.
I assume this might affect a number of other items with a unique (x) tag on them.