Very helpful. Oh yes, I am quite fastidious about not falling off the diet. It's just that the list of things I must add to the restrictions seems to grow.   

I know this post is old but was wondering if you ever resolved this. My son is in the same situation. Villi healed but gastritis / duodenitis remain and calprotectin elevated. Now testing for crohns which I am freaking out about. 

I did a little research and one kind of aphthous ulcer (aka, canker sore) is the Herpetiform canker sore. It is well-known that celiac disease can cause a skin rash known as herpetiformis dermatitis. I can't help but wonder if there is a connection. Celiac disease is also listed in this article as a cause for canker sores: https://www.mayoclinic.org/diseases-conditions/canker-sore/symptoms-causes/syc-20370615 Are you observing a strict gluten free diet? You might also look into reducing iodine consumption as that is known to help with herpetiformis dermatitis. Perhaps it will help with your canker sores as well. 

Do you wear an M-95 mask left over from the pandemic when you handle flour? Do you eat out in restaurants? Do you take vitamins?  

These articles are helpful.