I think I'm also going to place trash in chests now to actually bug test.
The first leading hypothesis was that the chests fell through the floor, but remained in the area. Hence, them being teleported Into the cave camp chests but not visible in normal camp.
Guess 1: long rest made sure the chests are now also in the travel chest above camp.
Guess 2: the cloning of the contents went wrong through subtracting and adding, e.g. +1/-1 owlbear eggs is zero owl bear eggs. Or, cloning unique items leads to problems, but my common items disappear, too, so that can't be it.
So either the game doesn't move your chest so much as clone it. Which can go wrong. Or chests fallen through the floor are prone to unpredictable behaviour.
My chests with the books placed inside it has only lost them once. I could fix this by loading the save of BEFORE loading the camp. This was on like day 7 and I'm at 8 or 9.
Edit: I should note that I took the chests out of the travel chests at this point before returning them. This might have unglitched them
