How can I edit a m4v movie file and retain subtitles?
Just a shot in the dark, but have a look at VLMC. It is a non-linear video editing suite based on the VLC library, maintained by the VLC community. Otherwise, another editing software program that I know works with subtitles is AviDemux.

Just as a note. I am pretty sure that if you cut scenes out of the movie, you need to edit the subtitle files as well (otherwise the timing goes off). Not quite sure if any of these programs take that into consideration and modifies the subtitle files for you.

Best of luck. Hope one of these programs helps.