Allergy or Stress?

My 3 yr old cat was diagnosed with Struvite Crystals. I took us several months but at long last 2 weeks ago he passed his urinalysis test. No crystals and a normal PH level!. The reason it took so long was his reluctance to eat the SD formula. I managed to mix his CD and SD until he was only eating SD which I believe helped to bring his PH lower. Now here is the new issues. Dublin (kitty cat) is licking all the hair off of his lower abdomen. I showed this to his vet who suggested that the mix of the CD and SD may have caused this and to watch to see if it improves on the SD only diet. There has been no change over the last 2 weeks. His still licks himself bald, but not to the point of breaking skin. Has anyone had their cat do this? Could it be a food allergy or a behavior issue? I would love any insight that I could bring with me to our next Vet visit. Thanks!!