I just went thru an awful ordeal with my toadstool.
What I learned from this experience and to possibly help others though I am not an expert and others may be more helpful/knowledgeable.
I have been reading and reading trying to find out what killed my toadstool (I also might have had a hand in that by trying too hard). These toadstool leathers are supposed to be hearty and survive everything. From what I have read, if there are spots on it, it is a wound, possibly by a predator. If the spots are not getting any bigger and you are getting good polyp extension, if it were me ( like I said I am not an expert), I would just make sure there is good flow around it, keep up with water changes and observe it to see if it heals itself and watch for a predator (snail, crab, worm, fish, other coral). Don't try to pick off the scabs. That stresses the coral more. Dipping stresses the coral more. I would just observe it for now. If the spots get worse and bigger and bigger, I would start reading up on cutting the infected piece off to save the toadstool. In your case being that your flow was turned off, it could have left it open to a predator or sting from another coral that ordinarily wouldn't have been able to get to it or something may have landed on it and irritated it. Observation is the key right now.