Honey is gone with the food on the table. I have no idea where it goes, but when i reset the game it's there. Also found out re-buying gets them to spawn.
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I also encountered the bug. If you buy honey and/or the bento box and afterwards end the investigation without consuming one of it, the entire item stack won't appear during the next loading of the map. If you don't own 4/4 yet, you can buy another copy of the item, afterwards the stack is displayed correctly. If you already own 4/4 you have to go into the SavaData.txt and make it less such that you can buy another copy.
I'm not sure if it can be replicated like that because it seemed to start to happen to me after a certain point in time, not sure though.