Yeah it can be a little complicated since you'll have to run a find command to say for example find /path/channels -type f -mmin +120 -exec rsync etc.....
If you have Channels set to create an edl file you could look for the edl file and then if you find an edl file next to the video move the video file over...
There's a few ways to do it, but the easiest is to just leave what you have where it is and then set the DVR location to your new external and your old location as an additional storage location. Then you can copy everything over and just delete it from your old location after the copy is done and you don't have to worry about finding new items and moving it.