No light kill bubble algae ?

[Doctorgori]

You can't pop the bubbles when manually removing. The best way is to use a small siphon tube with an angle notched out, to get into crevices. Use small enough tubing and remove like 2-3 gallons at a time. Try this for a few weeks. If you do pop them while doing this the siphon should catch the spores released. That's the key to overcoming it.

Supposedly the whole spore thing is not substantiated, but TBH if it were me, why take chances?
I 2nd the rigid airline tubing …I have used 1/4 and cut it at a sharp angle, also used screwdrivers, and paring knives …
also may as well go over the harvested areas with peroxide while you are at it

 

[Zoa.Mania]

I'd try api algae fix or vibrant before I’d restart.
You can also try some tangs such as naso or veliferum depending on you tank size.

From what I found valonia algae can survive for a long time under low light conditions. Idk what about no light at all but I doubt you can put absolutely 100% of your rocks at once in containers.
If you do, the containers would have to be connected to the system and even then the algae can survive in other places of your system such as overflow, sump, back wall etc..

So I think the best option is to treat a full system cure or control it with fish/inverts (if you can find pitho crabs that would be the best invert option, from what I know they are totally reef safe) and manual removal when needed.

Best of luck