Hmm well i wouldn’t think it’s the pellets. The draft from the windows being open at night might actually be the cause? Cycling fresh air into rooms can be good for their health, but usually you want to keep your rabbit away from air drafts for longer periods, especially if the air tends to be cooler at night. Bunnies generally don’t like to be directly in any cold air drafts.
It could also be pollen blowing in from outside irritating their nose/respiratory system… it’s hard to narrow down exactly. But occasional sneezing and a wet nose isn’t usually a huge cause for alarm. But I would maybe try closing the windows for a few days to see if it makes a difference? Maybe giving some echinacea tablets in water or alcohol-free tincture and giving her a little bit cause it won’t hurt.
Rabbits ears tend to be pretty cool! They control their body heat through their ears so reading their temperature from them isn’t necessary the best way (their ears are the best indicator for overheating, not so much for telling if they’re too cold). If you don’t have a thermometer, I tend to just put my fingers under their tummy since their natural body temperature runs pretty high so their bellies should feel pretty warm.