Library organization

[vad72is]

My movie directory in Jellyfin is E:\ and my shows directory is E:\Shows.

If the way you phrased that is how I'm interpreting it (that movies are in the E:\ drive without a sub-directory) then that's the issue.

Map your media using the below structure as a guide, then delete your libraries and recreate them with the new path.

Movie Library
E:\Media\Movies\
E:\Media\Videos\
E:\Media\DVD\

Shows Library
E:\Media\Shows\

Also, each show and movie should be in it's own folder within these folders, as stated documentation that TheDreadPirate linked. A screenshot of your folder structure with files would help if this doesn't immediately solve your issue.

Thank you, I mistyped my response here. My directory is E:\videos for movies and E:\shows for shows.

I did notice 2 things. My server log kept saying removing NCIS, the TV shows in question, and listed out the episodes in them in logs.

One thing I had wrong was my naming in that I kept naming the show so the file path looked like E:\shows\NCIS season 4\ ncis season 4 episode -name of episode. I saw on jellyfin that's not right. I renamed a few of them. I did a rescan and all the episodes are showing in the shows folder now. I'm not sure if that helped or not but they are showing there now. They are still showing in my movies folder now though. Babysteps I guess. Also I turned on NFO but  I'm not sure that helped.
I'd gladly show the directory if there is a way to do so. It isn't very big.
Thank you again.