When antibiotics are used for a specific infection with an inadequate or incomplete dose, sometimes the targeted bacteria can develop a resistance to that antibiotic. That’s why the instructions are generally to take the full course, even if you feel better. Pouchitis treatment is a bit different, since many bacteria are being “targeted” (even though we really don’t know exactly which bacteria would be best to get rid of or add). Nevertheless, over time a pouchitis antibiotic can sometimes become less effective (that happened to Cipro for me). Switching antibiotics every 2-3 weeks is thought to help prevent this, but is only possible if you have several antibiotics that work. Stopping (really switching) the antibiotics in this case doesn’t seem to reduce effectiveness.
Pouchbro, I don’t know what antibiotics you might be thinking of, but in any case it’s not generally true that antibiotics are so limited in how often you can use them, unless you have side effects or are approaching a toxic dose (e.g. enough to cause something like hearing loss).