I don't know about any long-term effects, but I do have one bit of advice - any time a dog is put on steroids, the drugs can cause increased thirst and appetite, which sometimes leads to increased need for urination (more frequent). JEB was on steroids on 2 occasions that I remember, and my sister's lab was on them for about 2 months for a leg injury that didn't heal, and both dogs peed in the house during their times on the medicine!
Another thing you might want to check in to is if your dog maybe has yeast or a food allergy.... Also, I know there are several posts on the board that list vitamin supplements and holistic treatments for allergies (just do a search).
Sorry I'm not much help - I hope Reeses is doing better soon!