It's more likely that any gnat adults flying around had already laid eggs in those other pots, or that those other pots already contained larvae from where they were growing previously. (If purchased in the past several months, that could have been the nursery.) Is any potting mix stored in a way that is not in an airtight container? If so, gnats might be originating from there. While the gnats can certainly fit through HVAC ducts and vent slats, it's highly unlikely that they are passing through any sort of air filter that is presumably in use in the intake vent(s) or on the HVAC unit itself.

Fungus gnats thrive in conditions of potting mix that stays too wet/damp. Check the plants that are suspected of harboring them before watering so that they are only watered when the mix starts to get dry enough, which for most plant species is at least an inch down into the container (though the depth will depend on pot size, with larger pots being allowed to dry deeper). Make sure any saucer or cache pot is also emptied of drained water promptly after the plant is watered, or otherwise it might seep back up into the drain holes and keep the lower levels of potting mix in the container too wet, killing roots and providing an environment for fungus gnat larvae to thrive.

Miri