Andrew McFadden said:Anything is possible
This is why I said leave the canister alone. Because by what your doing your going to destroy the BB in the tank or most of it anyway. So your best option is to turn it off while your doing the first cleaning. After your done turn it back on and keep a close eye on water chemistry and the fish for sickness.
Okay that's what I'll do. I was a little worried about losing too much BB since I just cleaned the filter two days ago before I discovered the nitrates had risen again but we'll just see how this goes.