If you read the R2R thread - the dose used (.125mg/L) that treats about 50% of the isolates of the bacteria that is claimed to be the causal agent (Arcobacter), especially depending on the species involved. (Maybe Arcobacter is not the pathogen) See article below. In human disease the LOWEST CONCENTRATION in the blood of CIPRO is 1.35 mg/L. This suggests to me (as the article says) - that CIPRO may not have done anything.
I know that others that use cipro for anemones use 250 mg/38.75 liters - which is a concentration of 6.49 mg/L. They also use a new tank - and re-dose every day. Cipro unless re-dosed in your tank is not going to last very long.
https://www.reef2reef.com/threads/how-i-cipro.211822/
As to changing the diversity of your tank - If you read the R2R thread provided above - they tested the genetics of the tank 3 times - before and after - and there was no change.
PS - no offense - and I'm not trying to be critical for the sake of being critical. One of the main causes of antibiotic resistance is using subtheraputic doses of antibiotics - in animal feeds, etc, etc. This is the reason that many countries around the world now allow antibiotic sales ONLY with the direction of veterinarians. So - with that also in mind, I think you're making a mistake. (and I have a degree in microbiology)