This issue seems a little difficult to replicate due to it relying on lag.
If you shift click to remove your bag from your chest slot or baubles slot while the server is lagging it will end up in your backpack inventory resulting in it being deleted.

I managed to do this with my bag after being killed in the twilight forest, my backpack was enchanted with soulbound so it stayed with me after death, i instinctively went to shift click my bag into my baubles slot as it auto equips to my chest slot. i quickly noticed the bag went into my bag didnt have time to take it out and it was deleted along with everything inside