Have a look at mkvmerge - specifically, the GUI.
Now, your chances for success depend a lot on the format. If it's high profile H.264, cutting is at best an inexact art because you should only chop on I-frames, and they're few and far between in a heavily-compressed file. Conversely, if it's MPEG-2, then chopping is much easier (and avidemux does a very good job here).
You'll need to play the file to find the right point(s), then split the file accordingly. You can then use either tool to append your new second part to the original first part, throwing away the bit in the middle (which is the overlap).
All this assumes that the files are the same format, though. You'll end up in no end of trouble if the image dimensions or sound track format changes at all.