Don't fret BigRedDog

Let me explain why I never clean my filter box itself. It's kind of a personal choice really. Although the good bacteria is on all surfaces of the filter and the aquarium most is found in the filter media as Griffin said. I want all of the good bacteria that I can possibly get so I do not clean mine. If I were to clean it, I'd do it in siphoned tank water and not tap with
chlorine in it. When I clean my impellers I use a Q-Tip and that's it. Putting your media in the tank while you clean it is great
Your cycle should not crash just because you clean the box itself (with filter media in the tank of course)
Hope that helps a bit

Ken