Describe the bug
When I remove some entries from the config file, they reappear once the game starts.

Expected behavior
I'd expect the config to respect my changes, even if these are removals.

Instead of removing items from the config file, put in an "no decay" entry. Example:
I:"foodfunk:rotten_food"=-1

This is due to the default values system that adds any missing default values to the config.