I have an mp4 container where the movie has subtitles that can be turned on or off.
It says "subtitles encoded into the Mp4s." and not hard coded so can be turned on/off
What program can this be done with, I presume it will work with srt subs.
Edit: i think it can be done with handbrake
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It's not clear to me what is that you need, exactly, to give you a decent suggestion.
For example.. you can put subtitles inside the container at encoding time but also without the need for re-encoding the whole video; if you only need to add subs to it you can simply REMUX it (adding the subs).. that's is a much better choice that doesn't affect source material.
To edit/convert/create subtitles there are other nice amazing tools, such as KaiNote.
You can find it in the software section of this site, is a totally free and open source software to easily mux/demux/remux files into the MKV container.
For mux/remux it has a very simple GUI you can use.. it doesn't re-encode anything so it's blazing fast.
You drag your video into the GUI, then you do the same with the subs...
Before remuxing you can change tracks name or set the appropriate language flag/indicators for them (and for audio and video tracks too) . MKV takes any information for the tracks from the source files automatically, if they're already set.
You have also an option to add specific fonts inside the mux, if your subtitles use them..
Then it's only to give the file a name ... press a button .. wait some seconds .. remux done!