Is there any discharge from his nose?

It probably is just the dust. If you see any discharge (clear is fine) then you might want to be concerned.

Are your food pellets “dusty”?  When I fill my small sealable container from the bag of pellets- I put the pellets at the end of the bag in a sifter to get rid of the “pellet dust” that has been created from some of the pellets crumbling.  Sometimes if they are snarfing their pellets down they can inhale some of the “pellet dust” and it is irritating to their nasal passages.

The pellet dust could be saved and you could use it to make bunny cookies- but I have never bothered- my bunnies already have tons of treats and cookies they love- and since they are given so sparingly, I have not bothered.

Similiar thought with litter too- I use Woodstove pellets and I usually take them outside to pour from the plastic bag into the storage bin- the wind helps blow some of the “pellet dust” away- and then I usually throw away the very bottom of the bag if it looks very powdery- and the same for the bottom of the storage bin.  I don’t want to introduce more “dust” into the house environment.

Is the air filter the kind that works like a fan, ie. it sucks in the air with particles than blows out cleaned air? (mine is like that.) If so, you might be pointing it at the bunny cage enough to blow some dust about an add to the sneezing. You can cool bunnies with fans as long as they don’t blow directly on them, but just circulate the air. I don’t know your set up, but maybe if it is a fan type, ajust it to be overhead if it’s currently pointing directly on Sneezy.