Many people who treat with cipro and amox have the same issues come back in time. Since the stuff only usually kills what is already in the corals or tank, there is no strange, dangerous pathogen that gets wiped out. The effect will likely only be temporary. I would still continue to look for the root cause.
If there were some kind of unknown pathogen, you also likely did not get it all with the cipro and amox and it will rebound too - don't worry about this since it the chances are slim to none and slim just walked out of the door.
New tanks can be hard. You likely will never know what really happened.
I appreciate the thoughts/info. I also have a UV sterilizer to plumb in to try and act as a control mechanism given my lack of precise diagnosis, in addition to a strict dipping (reef primer and KFC) and QT regimen. If it happens again, the only two things that I can think of will be to completely restart the tank after sanitizing or to do one of the genetic tests.