Existing files in library not showing up when scanned

Server Version#: 1.19.5.3112

I have run into an interesting issue. I was informed by my SO that some of her movies and TVs are no longer shown in the library. One example was that a mini-series only had 2 of the 6 episode that it had before.
I opened the player and had her show me the issue and and verified this. She also showed me how a few of her movies were no longer displayed at all.
I then connected to the Plex server and re-scanned the libraries, which had no affect. I manually connected to the file share and verified the folders/video files were on the server. After making copies, I deleted out the folders. Ran the scan again, and ensured the clean trash was turned on.
After this, I copied the exact folder for the mini-series back to the server and tried re-scan, this time the TV show did not show up at all when before it showed 2 episodes out of the 6.
I then tried to renaming the folders, and then the files, then re-converted them to a different file type, (from .avi to .mp4) and still nothing.
I then copied series that I originally placed in My Movies and worked but was actually a TV series, and moved it in to the TV section. Did a rescan and again, the movies do not show up.

I downloaded a random movie and added it to the system, re-scanned and still nothing. It seems as if the scan is not working at all.

Any ideas where to start?

TLDR:
TV and Movies are not being added when running a library scan.

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