I’m not sure if you’re still interested in trying to troubleshoot/isolate this problem, but if you are there’s relatively quick test you can perform.
Create a new movie library for testing. Add just one of your top-level letter folders to it (preferably one where you have movies missing in the existing library). For example, you would add:
F:\Movies1\C\
Before saving it, visit the advanced settings and ensure that Plex Movie is selected for both the scanner and agent (they’re the defaults, so they should be). Also disable all “extras” options such as trailers, “Find extras,” related external content, etc… Finally, ensure that “Prefer local metadata” is not selected.
After configuring as above, save the new library and let it scan. Given your new folder structure (each movie in its own folder) this should complete relatively quickly. When it completes, compare what you expected to see and, if movies are missing, check the duplicate filter in the library’s Library view:
The results of this testing will provide a good idea of what the new Plex Movie scanner thinks of your current folder structure and naming without all of the baggage from the old structure.
Regarding your existing library, it’s also possible that some items are also being detected as duplicates there. This could happen simply due to the renaming effort; with things having been moved/changed so much, Plex be confused. I think someone may have mentioned the Plex Dance above; it’s sometimes helpful to force Plex to “forget” about items after such sweeping changes.
