Sponge gets rinsed and thoroughly squeezed in old tank water and biomedia get rapidly dunked in old tank water. The HOB housing, impeller, motor, and plumbing get scrubbed under regular tap water with a filter brush.
Really? I feel bad now. It's been running for about six months now and I just take out the inserts and rinse them in tank water and clean the outside with my algae brush. I thought by cleaning out the body I would lose all my good bacteria. Next water change I will do the whole filter. Thank you.
You'll lose some of your beneficial bacteria by scrubbing the body, but it's not enough to outweigh the improved water flow you get by keeping everything clean. There are a lot of theories out there on cleaning your filter. If what you're doing is working for you, keep it up.