Renaming files

To recognize newly added subtitle files, you need to Refresh Metadata of the tv show (as a whole, not just a single season or episode).
The renaming might actually have triggered a new library scan, which sometimes achieves the intended result.

Sorry, what does that mean?
Which Linux distro? What kind of hardware?

Still doesn’t tell what kind of storage it is. External hard drive? Network share? Cloud storage?

I recommend you to solve your issue with the automounter of your Linux distribution first, before trying to tackle the other Plex issues. In essence, disable the automounter and create a manual mount for this drive, so the folder path to your media is always the same (and has always the same access permissions).

Unfortunately I am not a Linux expert, so I cannot tell you precisely how to achieve that. You might want to give this a look: Linux Tips