[Pantses]

Thank you for the tips, @Klojum. I did use the same MKV extension when I re-encoded and I had double checked the paths against what's in the database after I scraped it all again. One thing I didn't think to check was the paths in the database against what's actually showing in Kodi when I bring up individual episode info. It appears that my re-encoded files have a lowercase "e" for the episode numbering, which is accurately reflected in the database (you can check my previously posted export), but when I look at the path in the episode info it shows up as S01E06. I just renamed the files so they have capitalized letters and they are now playing correctly. I'm not sure where the missing link is, however. Is there somewhere else I should be looking for these file paths in the MySQL database, or have I discovered some sort of weird MySQL caching issue because the originals were S01E06 and new ones are S01e06?

[Klojum]

Linux is upper/lower case-aware by default, so S01E01 is different from S01e01. Windows, afaik, doesn't bother that much.

[Pantses]

Linux is upper/lower case-aware by default, so S01E01 is different from S01e01. Windows, afaik, doesn't bother that much.

Yup. I'm guessing that since the MySQL database is running on a Linux box and so are my files, that was an issue. The thing that confuses me is that the database seemed to have the correct case (matching the new files), but Kodi was showing the old case. Even stranger is that I hadn't accessed that series on one of my clients until I started troubleshooting this and the issue still persisted on that client. Even after fixing the names so they matched the original case, there was one file that refused to play until I gave it an entirely new filename (I switched S01 to S1). Is there somewhere other than the "Episode" table that I should check for residual paths in my MySQL database?

[Klojum]

Even after fixing the names so they matched the original case, there was one file that refused to play until I gave it an entirely new filen

From the top of my head, there are basically 3 tables: files, paths, episodes, with either just the filename, or the filename with a complete path in front of it.

[Pantses]

So the odd thing is that here's one that's playing correctly:
Episodes c18 lists: smb://BIGBOX/video/TV Shows/Star Trek/Season 3/Star Trek - S03e15 - Let That Be Your Last Battlefield.mkv
Files strFilename lists: Star Trek - S03E15 - Let That Be Your Last Battlefield.mkv
Path seems to list the directory paths correctly (smb://BIGBOX/video/TV Shows/Star Trek/Season 3/)

But the path listed in Kodi when I go to the episode info is: smb://BIGBOX/video/TV Shows/Star Trek/Season 3/Star Trek - S03E15 - Let That Be Your Last Battlefield.mkv
Perhaps the information in Episodes c18 is just not actually used by Kodi, and it's piecing together the data from the Path and Files tables?