This may be 2 years after the initial posting of this thread but the option offered above did NOT work for me. After poking around a bit, I discovered a resolve for this issue (that i've had myself a NUMBER of times) that's MUCH, MUCH, MUCH easier than entering/editing code...
* Open media, choose convert
* Select which file to convert BUT when you are still on the first page of the conversion process in "open media", there will be a number of tabs, (File, Disc, Network, Capture Device)
* Select "Disc" & you SHOULD see an option to choose WHICH subtitle/channel to hardcode to the file (if you know which subtitle you want to convert to the file, tick the arrows up or down to select that subtitle)
* Continue convert process as normal & when video is finished, it will have only used the subtitle you intended!
hope this is easier/quicker! Good Luck!