How to keep original softsubs (soft subtitles)?

[PJS]

I am trying to convert a large batch of anime. The audio needs to be converted from vorbis to aac to play on my Samsung television which does not support vorbis. The audio converts fine with mediacoder, however I lose the subtitles which I need because I listen to original Japanese audio tracks. I understand I can demux the soft subs in a demuxer program and then embed them, hardsubbed, with mediacoder, by pointing to the extracted text files, but this is a much longer process.

Is there a way to just copy/keep the soft subs during conversion in mediacoder? I'm not seeing the option anywhere.

If there is truly not an option for this and only hard embedding the subs from separate files, how can I do the hard embedding all at once in a large batch of 300+ videos with mediacoder knowing which subtitle file goes to which video? Or is one-by-one my only option here?

If you know of another program that can convert vorbis to aac while keeping the soft subtitles please let me know. (I did try Popcorn Audio Converter which successfully kept the soft subtitle tracks BUT it only converted the stereo English audio track and NOT the important Japanese due to being mono I think).

Thanks!