I have a bubble trap of sorts between my refugium and the return section.
I use the same type of foam block to mostly prevent the macro algae from getting into the return pump.
I know that while it may contain some bacteria, the tiny amount ( compared to the live rock in the tank) is not needed for the tank to function.
I do wait until I see the levels between the 2 chambers change. The more it clogs, the higher the water level gets in the refugium, and lower in the return section. I'll change it when I see it make enough difference to activate my float switch to the top off.
Then I clean it or just replace it.