FYI, perform an Empty Trash before you Clean Bundles (Plex Dance).
When you put the series back into Plex, add them one at a time. Let Plex finish sorting, adding metadata, etc for the first before adding the second.
If you continue to have issues, try adding a season folder and renaming the files (followed by a Plex Dance). Delete the DVDRip… type info from the file name or put it in square brackets so Plex will ignore it.
/A TV Library
/Salem
/Season 01
/Salem - s01e01.mkv
/Salem.s01e02.[DVDRip....].mkv <-- square brackets for other info you may wish to keep.
/Salem s01e03 [DVDRip....].mkv
Plex Docs -> Your Media -> TV Show Files (Naming and Organizing)