Thanks for the info. I'll probably end up doing them one at a time, though I have been looking around a bit and come across stuff like this thread https://forum.videoh...-MKV-container which has scripts in various languages, just not sure if I'm brave enough to try them out, especially as some of the fancier ones replace the original, which I agree is best not to do.
Some nice scripts in there, and some effort went into them. Parsing output in batch files is just too messy for me (I use bash, perl, python, and PowerShell mostly), so I applaud them for enduring that pain I'd assume most are fine with replacing files simply for storage reasons - if they don't have ample free disc space, they probably couldn't afford to take up a ton more with the new output files along with the originals.
Looking over them, it should be easy enough to identify and delete or comment out the lines that delete/replace the originals if you wanted to do that. Personally, I'd do them manually and take the opportunity to make your files' tracks more consistent to allow for scripted operations in the future (should you need to do so). For instance, all of mine have the native language AAC stereo mix as the first track, with the second track being the lossless or surround version, followed by any number of commentary tracks. This let me replace the AAC track easily when I needed to do so since I could always count on it being first. I did have a few that needed manual intervention (additional translation dubs, mostly), but those were few and easily found.
You could also add metadata to denote what the tracks are (e.g. "Director Commentary" for an audio track or "English Forced" for a forced sub), making it easier to pick what you want to see/hear during playback (Emby does show these labels in the clients). Definitely explore MKVToolNix's interface a bit - there's a lot in there that can be very useful.