Cold air tends to be very dry, which can most definitely irritate your nose and throat (among other body parts). That irritation and drying out can make the thin skin and mucous membranes more vulnerable to attack from bacteria and viruses.
The only really unscientific part of your post is that the cold air itself is not the direct cause of illness.
People with a strong immune system might not see a big difference, but if you are already more susceptible to getting sick, then the link to cold air may be more obvious to you.
It took me awhile to figure out the correct setup to get Sonarr, qbittorrent, and Jellyfin all to play nicely together, but once you get it figured out, it transparently addresses the problems of folder structure and allowing you to keep seeding content.
I had the same issue as you, initially, where I had to do a ton of library maintenance in Jellyfin. But since using Sonarr to monitor and import media from torrents to a structured media library, Jellyfin has been pretty hands-off