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This happened to me once: I put a HEPA filter in storage. While I was away the rood leaked and the box it was in sat in water for months! Needless to say the HEPA itself became a huge source of contamination - primarily molds, but also bacteria. I couldn't afford to replace it so I disinfected it: here's how - with formaldehyde.
I put several small dishes of formaldehyde in the blower, in the stuffing box ( the airtight zone after the blower and before the filter) and in front of the filter face. I sealed the whole thing in a tight fitting tent of clear plastic. I carefully sealed it with packing tape. I let it sit for 24 hours in the shade, and then the next morning I set the whole thing in direct sunshine to break down the formaldehyde.
After this treatment it was disinfected and I got three more years of use out of it.
A faster technique might be to set a dish of potassium pergamnate inside the filter assembly, and pour a little formaldehyde on it; toxic fumes will smoke out. Be prepared to seal those fumes inside the unit immediately - and hold your breath! Wait twenty four hours, and open in a very well ventilated area.
Vietnamese mushroom farmers using glove boxes often disinfect their glove boxes this way.