TV Shows appear in one Library fine but missing episodes in different Library

Plex DocumentationYour MediaNaming & Organizing Your TV Show Files

Your naming is incorrect. It does not matter that it works in another library. Basically, you got lucky.

Rename & reorganize per Plex documentation. Then Plex Dance the entire show.

/TV Shows <-- folder added to TV show library
../Star Trek Voyager (1995) {tvdb-74550} <-- year & ID optional, but helps.
..../Season 01 <-- "Season" in English.  Two digits for number.
....../Star Trek Voyager (1995) s01e01 Caretaker.ext <-- sXXeYY format mandatory. ext = mkv/mp4/etc.