Golden Bag of Holding sometimes, looks like it depends what slot it's in in your inventory, deletes all contents when in creative, including when you switch from survival to creative. I experienced this using Extra Utilities 2 version 1.5.2 in the current pack version

I see you have reported it on EXU2 github as well, thank you.

Apparently this looks like it's very common

So for now we could disable the bag OR just continue with the warning that contents are not safe.