I never made the pancake style myself, I used to make the fold overs often though. I found a Dremel with a finer grit sanding drum works like magic on those edges and fast. Just use a speed controller and keep it low-med and wear safety glasses!! Make double sure to hit the inside edges too if you have ANY love at all for your finish.
Also, a suggestion if I may; on the pancake style try a thinner Kydex, it will allow the holster to conform better to your hip area. Hmm.. I still have my Kydex press rig around here somewhere and some Red Kydex.. and a sweet looking Beretta I just picked up from Senior.. (excellent fellow by the way!) *sigh* another project!