Hey Brent,
Thanks for update and details. It may have been worth a call to Lionel for a problem that occurred on that many pieces of track.
In case you haven't discovered the method yet, when you pry the tabs up, use a large flat bladed screwdriver and try to do it in one move. Then, when it is time to rebend them, turn the track railhead down and press on it to hold the rail tightly to the roadbed.
The, place the edge of screwdriver next to roadbed with the blade parallel in the center of the tab. Bend it flat with a rocking motion levering off of the base. That secures it tightly. That will keep the railhead down.
It took a few tries to learn this when I started making custom cut length pieces.
I have attached the technique from the FasTrack Modular specification appendix. You can find the O gauge pin method there, too.