They are all in the one Movies folder, with some that are part of trilogies being in folders within that folder but these ones don’t seem to be the issue as they are much easier to spot.
The names all follow the Title.Year format so I don’t get why they wouldn’t show up.
One I have currently identified is Suicide Squad
Suicide.Squad.2016.avi
I have tried moving across drives, in sub folder, on its own, it seems like nothing can make Plex scan find the file.
Your naming schema is wrong.
That it worked in the past bears no meaning, because even back then it was not officially supported.
Officially supported is only what is documented here: Naming and organizing your Movie files | Plex Support
If you want to save yourself a lot of time I would recommend using Download - tinyMediaManager and use ${title} (${year}) ${imdb} as the new name format.
Make that ${title} (${year}) {imdb-${imdb}} (at least I hope it’ll use the curly brackets {} surrounding the imdb-id without further escape characters ).