This was driving me nuts. I wanted to transcode some MKV videos into H264/MP4 containers but these had subtitles so I used MP4Tools to do this. (MP4Tools is excellent, BTW!) However, I really wanted to use Submerge to alter the appearance of the subtitles to make them larger, use different fonts and colors. I did use some of the advice here regarding extraction apps but these were Windows apps and I wasn't satisfied with either the effort required or the results achieved.
Then I took a look at the options available from within MP4Tools and found an option that, during the transcoding, created a ".srt" file ("mux", don't "burn" the subtitles). I canceled the conversion and, sure enough, found a genuine ".srt" file that contained the subtitles. I was then able to use Submerge to do the transcoding and, at the same time, point Submerge to the ".srt" file with which I was able to specify the font, size, color, etc.
One interesting sidenote: If you simply "save" in Submerge, you'll get a ".mov" file containing the original video and audio along with a subtitle track. If the video is -way- too wide-screen (beyond 16:9), Submerge lets you letterbox the video (by adding a black mask behind the video track. Interesting thing about this: If the then open this video in QT Player Pro, you can change the position of the video track, moving it up so the subtitles appear -under- the video (in the black area). Now you can use Submerge to "export" to the H264/MP4 with burned in subtitles -below- the video. Bonus: The export also can be done using the El Gato Turbo264 hardware/app as it sees the subtitle track. Do note, however, that the older Turbo264 can't export anything much larger than 640 pixels or so; not good for 720 or 1080 videos.
Anyway, just wanted to contribute something back to Videohelp as a number of folks here have saved my bacon over the years. Thanks!
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