A bit of a late response here, but I find with Premiere that if you happen to have a file that’s corrupted, even if it’s just one, it can really screw up the whole project.
Try batch encoding all your raw/input footage to a lossless codec, my favorite on the windows platform is lagarith ( https://lags.leetcode.net/codec.html )
then simply replace all your footage in the project with the re-rendered proxies. This method has saved me many times. After Effects is a pretty good batch encoder if Premiere is still giving trouble.
Good luck!