First let Handbrake scan the mkv for forced subtitles using the "forgein audio search" option. I have found HB to do and excellent job of locating forced subs.
From the Handbrake website:
Forced Subtitles
With some DVD sources, there is a subtitle track which only displays during foreign language sections of the video. On some titles this is a unique subtitle track in the same language as the main audio track, on others it uses the standard subtitle track in the same language as the main audio track except marks a subset of the subtitles as forced.
In order to select this track, HandBrake can scan the source for subtitles that appear only 10% (or less) of the time in addition to scanning for the presence of any forced subtitles.
To enable this functionality within the HandBrake user interface, from the Subtitles tab select the Foreign Audio Search (Bitmap) option from the Track dropdown menu and click the Forced Checkbox.
If you do not get a foreign section only subtitle track in your output file, then you may have to manually find and select the correct subtitle track from the Track dropdown menu.
In order to determine which subtitle track to select open the Activity Window and look for the following text:
[10:08:16] Subtitle stream 0x20bd 'English': 421 hits (0 forced)
[10:08:16] Subtitle stream 0x34bd 'English': 1640 hits (0 forced)
[10:08:16] Subtitle stream 0x35bd 'English': 3829 hits (0 forced)
[10:08:16] No candidate subtitle detected during subtitle-scan
In this case you can see that subtitle 0x20bd should probably be selected manually. The subtitle numbers may be obtained by looking for the output of the scan, the number will correspond with where in the drop down menu that subtitle will appear in the GUI.
[10:07:40] scan: checking subtitle 1
[10:07:40] scan: id=20bd, lang=English, 3cc=eng
[10:07:40] scan: checking subtitle 2
[10:07:40] scan: id=21bd, lang=Italiano, 3cc=ita
[10:07:40] scan: checking subtitle 3
[10:07:40] scan: id=22bd, lang=Nederlands, 3cc=dut
[10:07:40] scan: checking subtitle 4
[10:07:40] scan: id=23bd, lang=Arabic, 3cc=ara
[10:07:40] scan: checking subtitle 5
[10:07:40] scan: id=24bd, lang=Bulgarian, 3cc=bul
[10:07:40] scan: checking subtitle 6
[10:07:40] scan: id=25bd, lang=Hrvatski, 3cc=scr
[10:07:40] scan: checking subtitle 7
[10:07:40] scan: id=26bd, lang=Dansk, 3cc=dan
[10:07:40] scan: checking subtitle 8
[10:07:40] scan: id=27bd, lang=Suomi, 3cc=fin
[10:07:40] scan: checking subtitle 9
[10:07:40] scan: id=28bd, lang=Greek, Modern, 3cc=gre