After renaming, you may need to Plex Dance the file. This clears out any matching info in the Plex Database.
Regarding episodes and ordering, Plex uses episode ordering from TMDB (aired) and TVDB (aired/dvd/absolute).
Check the ordering for Pokemon at those sites and see which one aligns with how your files are structured.
TMDB & TVDB frequently differ. For example, TMDB has 53 episodes for Pokemon Season 12, while TVDB lists just 52.
You can tell Plex which ordering to use:
Edit the show and select the appropriate ordering.
- At the show level (not season or episode) select the pencil icon.
- Advanced
- Episode Ordering (select desired ordering).
- Refresh metadata if Plex does not do so automatically.
Note: You can also change default ordering at the library level. Edit the Library → Advanced → Episode Ordering