I hope you washed it in aquarium water rather than tap water.
OMG..relax.
You worry about bacterial loss on your replaceable filter pads?
Whatever minimal amount of bacteria you have on the pads being washed with tap water will not throw your system into chaos.
Honest, it won`t.
OP,
Try putting your fish grabber net over the intake when you shut it off. Most all the pooh will stay in the net.
After cleaning you can try a turkey baster to get the gunk out of
the HOB tubs.
You could even rig a pair of nets to put in front of your outflow.