http://www.videohelp.com/tools/Video-Container-Changer
This is a portable simple GUI or front end for the cli [Command Line Interface] ffmpeg intended to copy the audio/video in one container, rewriting it in another container of a different type. You might use it for example to put the video on a DVD or Blu-Ray or whatever into a MKV file, assuming that's what your other software prefers. All sorts of container formats are supported. Caution -- using ffmpeg to change container formats is not foolproof, and depending on your source video file, choice of output format, & possibly the version of ffmpeg used, the results may or may not work. I wanted to write a post about it because when a ffmpeg re-write works, it can save you a lot of time & headaches, & since it is a re-write rather than re-encode, when it doesn't work you're not out a lot of time & effort.