You want it to work all of the time, well, frankly that’s just unreasonable
Unfortunately Plex is just kind of crap like that.
One time it decided that it only had episode 6 series 4 of bones, and none of the others even though they were sat right there in the file system, I could play them and everything from Windows. How did it manage that, no idea.
When it does stuff like that you just have to resync your library and eventually it’ll actually do it and start working again.