I know your issue was over a year ago, but on the off chance it helps: I’ve eventually been able to resolve a number of similar thorny issues by tyrannically enforcing extreme ultra-orthodox file & directory naming conventions. 
But before attempting any new remedies, I do first suggest that you completely remove the old directory from Plex Server, close/exit Plex Server, reboot the Plex Server machine, and all that other clownshoes junior-varsity horses@#t that comprises the “plex dance”… (If you don’t know what I mean, please search the forums and learn all about it before going any further.)
So starting with the old file you’ve called:
How to Build a Thriving Workplace A Leader’s Guide (TGC9648)/(TGC9648)_S01E01_ThrivingWorkplace.m4v
I can see any number of issues that wouldn’t usually cause any problem, but they don’t precisely follow the recommended syntax. For example, I know it doesn’t usually matter if the dir/file name includes an apostrophe (“Leader’s”) that the URL doesn’t:
https-etc-etc/courses/how-to-build-a-thriving-workplace-a-leaders-guide.html
I’ve got plenty of apostrophes in the fully functional file & directory names various courses, myself. But might this be an exception? 
Who f___nig knows with Plex sometimes, right? Sometimes the output just doesn’t make sense, and it’s not like we can inspect the code ourselves, as a community, to help figure it out what’s gone wrong (ahem). So instead you have to remove any such minor deviance with a burning and absolute zealotry; the word “overzealous” no longer exists here in this troubleshooting space. 
Next up, make sure to start each file name by precisely recapitulating the sanitized directory name of “class plus (class id)”, keeping the parenthetical id# in the exact same place after the full course name.
Another red flag: starting your filenames with an open parens “(” is another one of those tiny but weird, one-in-a-thousand-fatal-exception-causing deviations that need to be eliminated – even though, yeah, it’s right next to a thousand other directories that are already named the exact same way and have been working perfectly for months/years/eons. It makes no sense! But it doesn’t matter…
The underscore separators are another potential infraction: they’re usually perfectly fine, I know, but now they are unholy filth and must be scrubbed out!
(The only thing that doesn’t seem to matter is your pre-root directory structure, provided it isn’t excessively long…)
After the complete scrubbing it’ll end up looking like this – not “something like this”, please note, but precisely this, because if you follow all of the original Naming Commandments in their strictist form, this is what the result will necessarily be:
(pre-root dirs)/How to Build a Thriving Workplace A Leaders Guide (TGC9648)/How to Build a Thriving Workplace A Leaders Guide (TGC9648) - S01E01 - Workplace Well Being The New Frontier.m4v
It’s absurd beyond reason, I know, but by doing it this way I’ve managed, gradually and painstakingly, to sanitize into compliance almost every single exception in my own decently-sized TGC library. Good luck! (Also, it’s late on Saturday night and this entire post was a terrible drunken idea in the first place - but I’ll leave this tab on top so to remind me to edit it into a form resembling coherence sometime tomorrow. Until then, my sincere apologies to anybody who suffered through all that. Cheers! 
- CJ)
