I'm using MZ but the game started in MV. Switching to MZ seemed to cause a lot of issues if certain things were changed so it's a bit of a mish-mash of plugins of various version seemingly being held together by the digital equivalent of Scotch tape. A number are still MV plugins, which still work so I kinda don't want to mess with 'em (including YEP_ItemCore).
Setting the item as independent or not seems to have no effect. The main thing of being unable to use a food item for a set number of battles does work, which is the main thing I wanted with the favorite food thing being a bonus. It may be easier for both of us to just cut the losses rather than trying to figure out what exactly is conflicting in the rat's nest of plugins that rivals the mess of device cables behind my TV.