Hardcoding subs into an MKV file

[Slevin]

Hi there,

I'd like to merge several mkv files into one. A few of them contain forced subtitle, which editing programs such as Virtual Dub and Avidemux don't seem to handle. I therefore thought I might as well hardcode the subtitles into these files, so they should appear once merged with the others. However, I haven't been able to work out a way to burn the subtitles without having to go through the full process of format conversion with programs such as HandBrake. I tried MKVToolNix (which, supposedly, should contain this function from MKVMerge), and other methods suggested online, but so for, no good...
Please help...

[davexnet]

Burned in subs implies a re-encode because the subs become a part of the video stream itself

[sambat]

Does just setting the subs as 'forced' in MKVToolnix not work out?

[Slevin]

Multiplexing the mkv file in MKVToolNix with the subtitles set as forced doesn't seem to produce a file that would include subtitles when edited in VirtualDub, no.

[Slevin]

These are forced subtitles that cover all of but 2 minutes out of a 60-minute-long file.
Is there some tool that would re-encode only these 2 minutes, while leaving the rest of the file alone?