I'm really interested in this thread, as I often backup my disks (mainly BD), but lose the forced subtitle track.
I've commonly used eac3to to extract the HD video/audio streams, and the PGS streams as well, then re-mux to MKV. I've recently been experimenting with Clown BD though, which simplifies a lot of things. I'm also trying out converting to TS, which seems to be a good format.
What I am having problems with is the forced subtitles. I can check 'Force subtitles' in Clown BD, and have confirmed that I get an extracted .sup and .sub files, which if I open in BDSup2Sub, I can verify they are the correct forced subtitles with timestamps, but Clown BD (which uses tsMuxer) doesn't automatically seem to remux the subtitles back into the completed TS file, and I can't see an option to enable this.
Is there a preferred way to do this, or is there some step I'm missing? Certainly MPC-HC and TMT3 don't show the subs when playing back the TS file.