I have a video file split into three mkv files and I used MKVMerger GUI to merge the three files into one. The file plays fine but when I try to enable subtitles it doesn't work (using VLC player) the option is there to turn subtitles on but it doesn't seem to do anything. Before I tried to merge the three files the subtitles worked fine. Any input would be appreciated.
I doubt that MKVMerge will be able to retime the subs for you. You might have to do that manually. Demux your subtitle files, open them up in a subtitle program like Aegisub, Subtitle Processor, etc., and then copy/paste the files into one big one, and retime as necessary. ...at least that's how I'd do it.