This does happen because of Mildew and mold build up in the ducts and AC system.
I've experienced it a few times and I found this really helped:
1. Turn off the A/C and turn the heat to the highest setting and the fan to the highest setting.
2. Shut off all the vents so the air is trapped in the ducts, basically closing all your air vents, also you can set the air to come out on the setting where its NOT on your feet.
3. Let the system run for awhile, about 5-10 minutes.
Hopefully you should have cleared out a majority of the mildew and stink from it. Its not going to completely kill the mold or mildew but it should help with the smell. The A/C is the problem and like mentioned before, you should turn off your A/C before you shut off the car, or the moisture gets trapped.
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