Augmentin (and other antibiotics) aren’t usually used for cuffitis, though folks sometimes report benefit. Unlike most pouchitis, which can be wiped out by a two-week course of an appropriate antibiotic, cuffitis isn’t likely to work that way. Standard UC meds, ideally applied locally, can treat cuffitis with fewer side effects. For example, Canasa suppositories are often helpful. Sometimes local steroids like cortifoam are needed.
You can have both cuffitis and pouchitis. It sounds like they probably saw pouchitis in June.