Most dogs will change over easily within a weeks time. Any signs of trouble, just back up for a couple of days.
IMO, you did not screw up her digestion for good. You might want to advise any future vet if she has had a number of antibiotics (and keep a list) in order to let him/her know that they might have to start with a start with a different one in the event of a future infection of any kind. (And, of course, you'll never quit an antibiotic regimen partway through.)Woody Taylor said:Biggest mistake I made with my dog was getting her and having her for a few weeks before I found the Leerburg site and forum...she developed coccidia, I did the full range of antibiotic treatments repeatedly (she kept getting parasitic stuff and none of us figured out at first some of her fecal tests were showing parasites that didn't attack dogs) and stacked immunizations on top of them (all the while feeding her all the greenies she could stand). I'm convinced I screwed up her gut for good with that bit of owner ignorance.