So, I ran s04e01 and s04e02 through HandBrake. I just did the default preset for MKV (because it takes 1 second to write the tags compared to mp4s that have to re-write the whole file apparently, but I digress).
The new files show up seemingly fine and can have their filename converted to tags. Success!
I just wanted to throw this out there in case it made sense to anyone else. I realize there is probably a lot more troubleshooting to be done (which codec? how was it encoded? etc.) That I may not have the time or patience to really dive into.
I also wanted to mention, that if I click on one of the RED X files, the icon will absolutely change to the Orange Cone (VLC Application if you didn't know). I think that's a little weird that it changes. Sure, it's nice to know which application is associated with the file type: MKV, but if the file is not going to be recognized, then I like to see the RED X stay as the icon until the file is compatible.
I hope this makes sense. Cheers,
-J