He's back up over 40 lbs again, only 3 pounds below where he was in July. I'm just letting him eat. As long as eats his healthy food, pasta, fruit and cheese... I let him eat some crap. Gluten free oreos, homemade muffins that seem like crap, but are actually quite healthy (at least compared to gluten free oreos).
Feeling mighty relieved. I plan on keeping him on probiotics indefinitely.