Repacking subtitles only from source MKV to existing MP4?

[funkyfolkrocker]

Hello! New here!

I've become somewhat proficient with FFMPEG and typing up batch scripts for converting recently. My issue is... I refined my batch conversion options to produce intended results (going from mkv to mp4). I'm about 48 hours into converting and... I realized my subtitles option was incorrect and am missing subtitles on all of the mp4 output files.

Is there any (relatively) painless way to simply import/repack subtitle streams directly from MKV files to already existing MP4 files?

I've stumbled on MP4Box and started working out an FFMPEG script to (re-mux?) the already transcoded MP4 files, but I don't quite know if what I have in mind will work without having to re-encode everything all over again from the start... And I would rather not spend several days doing that again.

Using FFMPEG, Handbrake, or MP4Box via command line (with broad scope target syntax? Eg: %%F) would probably be prefered, as there are many files that need subs transferred. If I have to repack from MP4 to MKV, transfer sub streams, then repack back to MP4 again that would be fine too. As I'm imagining that might be necessary?

I've tried searching for solutions to this issue, but almost everything deals with transcoding or conversion rather than simply importing a stream to an existing file.

Using Win10. And, it might be worth mentioning that I did re-encode the MP4s. So there is a difference in video bitrates and total filesize between the two formats. In case subs might be controlled by that factor.

Looking at MediaInfo comparisons between one MKV and MP4, the subs look like they did actually get transferred.

I used

ffmpeg -c:s copy

by mistake while transcoding / re-muxing?

The MKV subs are in VobSub format, with Codec_ID: S_VOBSUB
The encoded MP4 subs are in VobSub format, with Codec_ID: mp4s-E0
But, I am unable to toggle them on/off while the MP4 is being played.


To reiterate,
I'm wanting to import/repack/merge subs from multiple MKV files (all of which have only one subtitle stream), into existing re-encoded MP4 files in softsub format. It looks like the subs are already present in the MP4 files, but aren't able to be toggled on. Maybe there's a simple edit command that can flip them to the proper format within the MP4 files?