I think it does mean that the Cipro is probably no longer doing the job. Was he having any other symptoms of pouchitis? It can creep up so slowly that it continues to seem “normal” even things get appreciably worse over time. Has he tried other antibiotics? Ideally he could find another single antibiotic that would do the trick. It’s also possible to get good results with a combination of two antibiotics. When Cipro alone stopped working for me (something like 7 years ago) I was able to get back to a very good situation by adding Flagyl, even though Flagyl alone had never helped me.
The fissures might be something else -perhaps he’s straining?