Neat trick I learned at Riders Services on Cycle Oregon - nail polish. Stitch the shorts up with needle and thread like they were quality cloth that could handle the stitches. Then brush clear nail polish over teh stitches and up into the adjacent fabric. Nail polish is is a good quality, strong glue and comes in nice small containers with perfect little brushes. Only drawback - it's a little odd going through checkout.
In fact, I just got back from 50 miles on that pair of shorts and that repair is several years old.
Ben