Actually, your initial reply was very helpful, because it reminded me I had the JDownloader install but had never actually installed it. Once I did, and used that instead of going through Youtube's onsite downloader, the problem immediately became clear. Youtube's onsite downloader only grabs a compiled mp4, so when I downloaded an episode, it included the subtitles as though they were hardsubbed.

Once I downloaded the exact same link through JD, I got the bundled files, and was able to do a swap. I'm checking to see if the Orange Biscuit subs in this same playlist are hardsubbed. I don't know if you're planning to eventually do all the eps, but I want to be able to swap in your subs, if you do.

So, no need to upload more files. Thank you for being willing to go to the trouble, though!