I only read about three pages of this thread and it keeps coming back to the AC110s on the 90 gallon.
Get rid of them and buy a canister that holds more bio media. AC110s are junk when it comes to bio filtration on a large heavily stocked tank. Especially when your using chemicals which convert chlorimines to ammonia.
You don't need to shut your filters off when doing a water change. With that said, I have shut my canister off for a couple hours without injury. I would not chance that at all with a HOB filter which removes water and food from the bacteria.
Before dumping water into your tank, I would treat it first. Maybe get a trash can or something which can hold lots of water, enough to do a 25-50% water change. Treat it and test it to make sure its good before putting it into the tank.