I'm going to guess that mom cleaned it up, but it's still sick. Can you listen carefully and observe to see if you notice one wheezing/sneezing? If the weather's not too bad, you could sit next to the hutch with a book or something quiet to do...I'll bet the sick one will become apparent...
Could your bun have been out of the box in a draft for a short while? Hoping it's caused from new straw or hay, or it could be caused from a sensitivity to slight nest box odors. Hoping it's something that has cleared up perm.
It's been below freezing here so my nest boxes have been left in, which makes me nervous to do, but the bedding has been changed out every day to keep down as much bacteria and stress as possible. It was rainy here for a few days and I've been sick, too, and treating a 3 wk old kit with an eye infection. Not sure how that's gonna go. I hope all the best for you and the kits.
It's probably time to clean out the nest box and replace it with clean hay. All that hair in there can be problematic, but agree with earlier poster that you need to be listening to the lungs. It could be several different things, some contagious and some not. Here's a good resource http://www.bio.miami.edu/hare/sneezing.html
You might also check for proper teeth alighment. Do your bunnies have chewing sticks in their pen? What time of day did you find this problem? It may have been after mother's feeding time, although about this time, many mothers will be weaning their young.
Hope this helps and have a blessed day! It's time for me to go relook at nest boxes with very young in it and remove some more bunnyhair blankets... My moms are good to keep their young warm but sometimes just wayy too much but I'd rather they be Good moms! Nancy
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I checked on them all 2 more times yesterday evening and 2 times again this morning, sat out there with them, and everyone seems healthy as an ox. I changed all the bedding in the cage and nestbox again... No discharge, no runny noses or eyes, no crusties on feet... I even picked each one up individually and looked them all over and listened to them breathing... I just don't know. Maybe it was allergies, or milk or who knows!