Cameron, sorry for the necessity of putting them down :grouphug2:
As for housing for the new stock in your barn, in the winter when the doors are mostly closed, and only feet away from where the ill stock were held ... well, I would suggest that you clean, clean, clean EVERYTHING the ill rabbits came in contact with: cages, feeders, waterers, etc. with amonia/water and let dry ... in the sun for an afternoon if you can. Then, douse the soil where the cages were with diatomacious earth or lime dust or seven dust to be absolutely sure the pathogens are killed.
Then, when you bring your new stock in and get them set up, you want to either bring in the EXACT same feed the breeder was feeding, or transition them to your feed by putting them on oats and grass hay for the first couple of days to help them settle down without adding in shock from changing feeds. Then, start adding in pellets at 1/4 cup increments ... one 1/4 cup in the morning, one in the evening, one the next morning then 2 that evening, etc. This will give you an opportunity to observe them closely and if you see ANY distress, seperate and quarantine that one. Hopefully, it will simply be an allergic reaction to the new environment. Even occassional sneezing is not necessarily pasteurella, but certainly warrants close observation and quarantine until the cause is determined.
I wish you all the luck in the new stock!!!