Is your new rock wet live rock or dry rock? If its live rock you can do a full rock swap in one shot. If its dry rocks, I still think you can do it safely for a 32 gallon with only 3 fish. The majority of the bacteria is on the rocks, but there is still significant bacteria on the sand and glass and filters, etc.... if you have some rubble or ceramic bio media you can add to your filter that would give some extra precaution.