I've been playing around with the idea of dipping or dosing my macro tanks with something prior to the move, just to get rid of any major diseases I might have in the tanks. Fairly positive that they don't have brook, ich, or velvet, but uronema (probably present but not causing disease yet) is probably going to be an issue, since I'm not sure what I can add to the tank that will treat for uronema, but will leave the macro alone...
I debated trying to eradicate any Vibrio and/or Mycobacterium that may have gotten into the tank, but I'm not sure if it's worth the effort at least for the Vibrio, since it comes in with the frozen food...
It'd probably have to be some sort of multi stage dip/quarantine. Keep the chaeto fishless for a period of 76 days to starve out the velvet, ich, and brook. Fenbendazole to take care of hydroids/aiptasia. Metronidazole maybe just dosed to high heaven to take care of Uronema. Praziquantel, or better, piperazine would take out all worms. Of importance though, is that I don't know how the macroalgae would react to any of these medications. Assuming they react well (and don't die), that would only leave bacteria and viruses...
Of the "bad" bacteria, I'd only focus on Mycobacterium marinum. Vibrio's probably already in most systems just because a lot of people feed frozen non-irradiated food. For mycobacterium marinum....I'm stumped. Human medicine says that the best treatment is clarithromycin + ethambutol, but good luck trying to get enough to dose the tank....