Those images show the libraries and using Anime as an example. in the pictures above only the Anime in the /home/plex-box/Desktop/plexmedia/Anime show up in the plex app, nothing from the other path (/secondary/plexmedia/Anime)
Any help? Also running this on Ubuntu 20
Also if this helps here is a screenshot of both directories on the server:
I can’t see the names of the files in that image looks like just the folders. It could maybe be permissions issues on the individual files.
You have that anime library set as a TV library and they need to be organized and files named like a TV show they way the server expects them to be.
A tv library need the files to have the season/episode notation like S02E02 for the files else they will be ignored. ( there can be other similar notations that work but best to stick with that). The server will ignore files it does not think are TV episodes since it won’t know what season/episode number to assign them. For movie library it will ignore files with that notation since they are not movies.
If you don’t care about Plex treating them like a TV show you can use an “other videos” library type instead. but it won’t grab online metadata and won’t do things like autoplay or put the next unwatched episode up on home screen