Rotating antibiotics only works among antibiotics that are effective for you (or your son in this case). If an antibiotic doesn’t work (for pouchitis) in about a week it’s probably time to *abandon* it (I wouldn’t call it “rotating,” though).
If you re lucky enough to find a few antibiotics that work, it’s best to rotate them every 2-3 weeks. In theory that would help prevent them from losing efficacy.