Plex Missing Some Episodes on Scan

Im trying to add some kids TV shows for my kids, all the files are the same format but a chunk of them are not showing up after a scan library files.
I had uploaded some files earlier and deleted them through Plex so I could upload higher quality files. Now when I try to add the higher quality TV episodes they don’t show up. Episodes that were not there before are showing up just not prev uploaded video files.
Any ideas how to resolve this?

Problems like you describe are often (about 85-90% of the time) attributed to naming or structure.
So how are your file named, exactly? And what is you exact library structure?

This is the info I often post when I suspect naming problems:

TV Shows <— The library points here
---------TV Show Name (Year first aired if needed) <— This folder holds the season folders
------------------Season 01 <— This folder holds all the episodes for season 01
-------------------------ShowName - s01e01 - Episode Name.ext
-------------------------ShowName - s01e02 - Episode Name.ext
-------------------------And so on for the rest of season 01
------------------Season 02 <— This folder holds all the episodes for season 02
-------------------------ShowName - s02e01 - Episode Name.ext
-------------------------ShowName - s02e02 - Episode Name.ext
-------------------------And so on for the rest of season 02
------------------Season 03 <— This folder holds all the episodes for season 03
-------------------------ShowName - s03e01 - Episode Name.ext
-------------------------ShowName - s03e02 - Episode Name.ext
-------------------------And so on for the rest of season 03
---------2nd TV Show Name (Year first aired if needed) <— This folder holds the season folders
------------------Season 01 <— This folder holds all the episodes for season 01
-------------------------2nd ShowName - s01e01 - Episode Name.ext
-------------------------2nd ShowName - s01e02 - Episode Name.ext
-------------------------And so on for the rest of season 01
------------------Season 02 <— This folder holds all the episodes for season 02
-------------------------2nd ShowName - s02e01 - Episode Name.ext
-------------------------2nd ShowName - s02e02 - Episode Name.ext
-------------------------And so on for the rest of season 02
------------------Season 03 <— This folder holds all the episodes for season 03
-------------------------2nd ShowName - s03e01 - Episode Name.ext
-------------------------2nd ShowName - s03e02 - Episode Name.ext
-------------------------And so on for the rest of season 03
Note: The year after the show name is only normally needed or desired if there is more that one show with exactly the same name. Check http://thetvdb.com/ if you are not sure and match exactly the name used there. There are some exceptions to this where the year is needed even if there is no other show of that name or if the show does not have the year in TheTVDB.
There are naming methods other than the above that work but this does work 99.9% of the time.
If you are going to use Plex it is best to use the proper naming conventions so Plex makes the best match possible. Trying to force Plex to use other naming methods is just asking for frustration.
https://plexapp.zendesk.com/hc/en-us/articles/200220687-Naming-Series-Based-TV-Shows

I hope that helps.