Including the year is recommended with the new agent as it’ll give you better matching results (though make sure to use the correct year the show first aired!). In tricky cases like yours you can also include a reference to one of the online repositories.
Example
TV <- the folder linked to your tv-show library
The 4400 (2004) {tvdb-73507}
Season 01
The 4400 (2004) - s01e01 - Pilot (1).ext
The 4400 (2004) - s01e02 - Pilot (2).ext
The 4400 (2004) - s01e03.ext <- episode title is completely optional
...
4400 (2021) {tmdb-127581}
Season 01
4400 (2021) - s01e01 - Past Is Prologue.ext
4400 (2021) - s01e02.ext
...
As your files are already matched (and incorrectly merged), you should do a full Plex Dance (of which you already did some steps; make sure you do all of them!)
