Okay, I know it's been a month since there's been any discussion in this thread, but I'm circling back because I figured out what the reason for the disappearing meals is. I wanted to post it here in case this comes up for anyone searching the same 'problem' in the future.
If I visit a residence with a played sim from a different household, then the meals that were out on counters will all be gone when I rotate back to the household who actually lives at the residence. I believe it is caused by the same clean up scripts which clean up food, plates, cups, glasses, etc. on community lots between visits.
