From my experience with Effective, successful Hyposalinity treatements, your bacteria bed wherever it may exist (i.e. in your bio-wheel, substrate, even live rock) will NOT be affected.
BUT, be advised that HYPO at the correct salinity (i.e. at or below 1.010) will kill all inverts, pods, worms etc. in your live rock or substrate for those thinking of doing it on their main tanks and not setting up a separate Q tank...
I did my main tank but removed all the inverts I could find and my limited quantity of live rock. AND note that I still run a sump with bio-balls so removing my live rock did not impact my Nitrogen cycle (waste processing)...
One has to put some thought into Hypo prior to execution! but... it is 100% safe and effective if done properly... (i.e. with refractometer, buffering the pH, etc.)
Good luck!