I renamed a few folders and moved some files around and things are back to normal now. Indexing is working again.
I am having close to this same problem. I have a 16 TB NAS connected to the newest version of plex server RUNNING ON A Windows Pro machine. i have several folders such as Movies, Movies_2, Christian_Movies and more. On my web interface I can see all movies in all categories (folders) but on a couple remote connections Movies 2 shows up but says there are no items found in his library. I have made sure they are shared and the movies show on the server interface as well as the plex.tv web interface Please help. I have rebooted the server several times. I am thinking about rebuilding the server on Linux as my last server on Linux ran much better and I didn’t have these issues. Your opinion on this?
I can confirm the naming had something to do with not having any files seen by the PLEX application from my NAS.
I too also use PLEX for many years, i’ve used it on an old NAS with Windows7 and had no issues with adding files or folder paths or drive paths to it.
I’ve also used it on my old NAS even with Windows10 and had no issues.
But now, since i’ve did a hardware refresh to my NAS and have a new build, have the same Windows10, i seem to not understand why from all of the sudden the Plex does not recognize files that he used to recognize in the past 
It’s just mind-blowing
But i have to be honest, i don’t have a good patience level invested in my by God so i won’t stay and troubleshoot this for a longer period of time
That been said, i read what has been said above, noticed that somebody said something about renaming the files, tried that and surprise… it works :))
Don’t ask why, i don’t know and as said, i don’t have the patience and nerves to investigate
What i have to do now is start renaming all my files from my NAS but i have to convince myself first to do this, cause it’s gonna take a while
Just wanted to share this with you guys and confirm that by renaming the files, the Plex app recognizes the files.
Peace out, be safe !!!
Look for software called “filebot” to make that process easier.
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