It should be possible with an audio filter to some extent.
You mean that I could:
1) create an audio track containing a beep every two minutes, with the same length of the movie
2) extract the audio track from the movie and merge it with the beep track
3) create a new movie with the new audio track and the old video track
Is it right? It's not very easy since the file is 20 GigaBytes large...
EDIT: I read your answer again and I realized that you probably meant something different... Did you think about a particular audio filter that I could try out?
VLC on Linux Mint 17 XFCE. English isn't my first language, so please excuse any mistakes!