Apologies for reporting this again but it seems the bug has somehow returned completely at random for me?
I did a new playthrough, things disappeared/got looted as they should have... but then hour later when I did some backtracking and returned the same area, the lootables were again there, the doll was in the dungeon again etc.
What is strange, that this seems to happen only on things on the ground (doll, mushroom, herbs) and boxes. Shelves, chests and tables will remain empty.
What is even more strange, that areas that I just recently visited would still be empty. This would happen only to areas I haven't been to for a while.
Any idea what is happening? I am on 1.0.6 stable still.