Convert .mkv and keep subtitles

Xubuntu 14.04, up to date.

I have an .mkv file of a video in a language that I do not speak. The video includes optional (not bued in) subtitles in English, which are vobsub. It plays just fine in VLC (no error messages). The file is 6.6 GB and I wish to shrink it to about 1 GB. Normally I would do this in Handbrake, but Handbrake will not open the file; that is, it appears to open it, but the GUI still says New Video and it clearly has not imported the file.

I can successfully convert it to a new .mkv with mkvmerge-gui, but the subtitles get stripped out of the output file. This, in spite of the fact that the subs are listed as vobsub in mkvmerge-gui. I tried Arista, but again the subtitles get stripped out. Ditto for winff. I also tried Avidemux, but Avidemux will apparently only encode subs if they are in a separate file. I have DVD:rip, but I have never figured out how to use it.

I need some suggestions. I'll try anything.