As I was reading this article, I started thinking, "what we really need is a surface area you can extract and expand", and the image of a roll of corrugated material came into my head. It's a lot of surface area in a cylindrical space, and when unwound you have substantial access to the surface. No nooks and crannies that you can't reach with a simple tool.
The other route to go is what the pool industry does, which is to 'shock' the system, which essentially means to poison the microbes in such a way that they fall into suspension and you can filter them out (possibly with a separate filter so you don't foul the standard one). But that shuts the whole system down for some time. Not a showstopper if you can rotate out reactors, but I think you'd be better off with a replaceable parts mentality, swapping out parts for maintenance and cleaning and bringing the system online faster.