For the actual question: you probably leave the filter in place until it's clogged, at which point you replace it as normal except you're wearing a hazard suit. Those filters basically don't let anything go. However, note that the filter will be exactly as contaminated as anything else on the outside of the car is; a persistent weapon will have covered every surface in the attacked area with hazardous numbers of spores or similar, not just the filters. If it's not a persistent weapon - that is, it's designed to kill or incap everybody and then dissipate so your soldiers can walk in two days later and take over - then you just wait those two days.