As a note: getting all conditioned live rock would help your algae situation. Phosphate (algae fuel) comes bound to new rock and sand, not just on the surface, but deep into the structure, and when it gets wet, it slowly soaks out, a process that can take 2-3 years depending on the size of the rock. As it soaks out and gets into the water, algae grows. Phosphate uptake (getting it out of the tank) is expensive and time-consuming.
Replacing problem rock with better rock is not going to hurt your tank, but it does point to a lack of tank maturity that will require some careful management. Best start is to stabilize your water parameters pretty well like mine in my sig line, and use dosing and water changes to keep them there. When something grows to the detriment of things you want in there, it's called a bloom, and blooms happen only when there's too much nutrient for the bad thing and not enough balance. Hope that helps.