Ive been able to avoid it recently by taking precautions

However, while looting and not paying attention and moving items into a Soph. Shulker by just drag dropping in items leads to an unstable reaction. 

Item in slot > left click item > right click item (drops into Soph. backpack or shulker via mod) > ? > Profit 

Ive been circumventing item loss recently by repeating the above process however afterwards I hold Shift, and watch the inventory update to include the item recently dropped, if needed we can get together and i can recreate the scenario.

Ive just been taking screenshots of the inventory if anything critical disappears recently.