The HEPA filters can collect mold and mildew as part of the process. The mold goes through the dirty side and gets filtered through the filter material and pretty much stays in the material until changed. This gives it the opportunity to grow, especially if you turn off the air. Well in our facility at work, we shut down for a month out of the year and change out the air handlers' HEPA filters annually. In your furnace, you change out once a quarter(4x per year). I would only change these ones out annually or if you smell something you shouldn't. If you are sensative, you may consider every six months or sooner. I guess it depends on how sensative you are.
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