While there may be a technical way around this, an easier way would be to cut your MPEG at the 99th film (Or 98th, so you can put a chapter stop at the end to allow skipping over it), and the remaining segment would start over with the chapters. You can link the 1st segment to the 2nd so that it will automatically start the next segment if you were watching all the way through (the pause would be minor.)

If you still have the videos in Vegas, then just make two new MPEGs. Did you have any other Vegas questions?