i dealt with the outbreak of bubble,(and other, nuisance algaes), both small and large, in my reef tank, when it was starting to go through the various algae phases, in the following manner (a 75 gal. w/about 80-100 lbs of rock):
turned off all pumps (in order to keep as much 'sediment' from getting blown off the rock and back into the tank as possible)
lifted rock gently and slowly out of tank, and placed the pieces in the sump, and in buckets, that i then filled 1/2 way w/water from the tank.
'scrubbed' each piece of rock thoroughly, w/a toothbrush
rinsed each piece by dunking and swishing repeatedly in the sump and the buckets
replaced the rock back into the tank, and then added new sw (rodi) back to the system, to replace the 'rinsing water'.
almost none of the life on the rock was harmed in any way-with the exception of some small patches of (millepora?) sps colonies that came in on the rock-and not all of these were destroyed, either :wink:
after 4 of these 'overhauls', no more nuisance algae problems (including bryopsis)
took a few aspirin after each time, though, for back pain :wink:
valonia should not be removed in tank, imho-if a bubble is popped-spores get released back into the tank.
when it was first suggested to me that i scrub the rock, i was fairly hesitant -intuitively thinking that i would kill off many critters.
after trying it and seeing for myself just how tough the life on the rock really is, i started to recommend it to all of the customers i took care of while working at the lfs, where the 'technique' was first suggested to me.
this is also how we periodically managed the lr in our holding tanks-which were abit too overcrowded w/rock in relation to the volume of the system.
after each 'cleaning'-it appeared as if the coralline growth even improved dramatically, and a few days later, greater expansion was noticed on the various hard and soft coral 'bonuses' that arrived 'still on the rock'.
hth