I’ve been told by my doctor that toddlers (he’s almost a toddler) can have diarrhea for weeks after a bout with a stomach virus. They even call it “toddler diarrhea.” It can take that long for intestines recover. Also if you had a stomach/resp bug, it could have been Influenza A which can last two weeks in some people.
It is possible that the small amounts of dairy is the culprit. If I am remembering correctly, from what I’ve learned on this site, most kids will not outgrow MSPI by 12 months of age. Also, it can take weeks for the milk proteins to build up in the body and begin causing symptoms, so he may tolerate yogurt and cheese for a while and then begin reacting to them.
I would be concerned about his fat intake at this time. Until he’s 2 he really needs the fat content in whole milk or a toddler formula, so I’d definitely talk to his doctor if you are not going to go back to adding flax or olive oil.
Sorry I couldn’t be more helpful.