will this cause problems??

[meltdownaverted]

With any big change there will be a cycle. Might not be a big one but there will be a spike. The major thing is you are cooking all but a few chunks of your live rock, which means dead rock with only a few pieces to reseed it. Might be a better idea to cure the problem instead of concentrating on the symptom. The few pieces on rock your corals are on will still have traces on algea anyway.