I'm going to be removing several from frag plugs this morning. What I do is get a rinse tub with tank water then pull the plug and scrape off the bubble at it's base. Once all are removed then swish the frag or coral around in the tank water before returning it to the tank.
Yes but #3 won't help. As stated, rinse in a container with tank water. If the bubbles break you don't want the spores in the tank as that's how it spreads.
If your very careful, some have brushed hydrogen peroxide on the frag plug to kill any spores. Just be care not to get any on the coral. If I see any, and I can't remove the rock, I have used a very tiny syringe like the ones use for an allergy shot, and injected hydrogen peroxide into the bubble. It kills the bubble and spores.
The peroxide will work, be careful around the coral though, but a little bit won't hurt it too much. I used a toothbrush and peroxide on my old set up before and it worked.
Yes I'd do peroxide on the frag plug and/or exposed calcium skeleton if they are attached there. Or pop your coral off entirely and replace the plug. You want to avoid BA at all costs.
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