When I clean my reactor, I keep the bio pellets in the tank water that remained in the reactor when I removed it for cleaning. Just dump the pellets and tank water in a small bucket while cleaning the reactor and when you've finished cleaning the reactor, replace the pellets and tank water back into the reactor. You should complete the entire process as quickly as possible as you don't want the pellets to remain dormant for too long. I also use this opportunity to soak (in vinegar & water solution) the pump during the process. I've cleaned my reactor this way a number of times now and have not noticed any immediately increase in N or P.
