When I transferred tanks, my rock had tons of bubble algae. I removed it manually one piece at a time as the rock moved over. The new tank was clean enough that the algae never regrew once there. i imagine doing the same but in the same tank would work.
As for FW killing the worms, i think you'll then have a bunch of rock with dead worms in it, which will really contribute to further algae problems. Again, moving to a new system without food for the worms will slowly see them decrease as they starve themselves out. No spikes that way.
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Brad
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