I built that same pistol model years ago. We had that same problem. It was a hassle but we fixed it with holding it in place while coating it with a light coat of fiberglass resin. After that, we used a rondo technique to harden the model from the inside.
It's a great file, but warping is something that is going to happen with small or large pepakura weapons. Hope this helps!
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I believe the file is on thingiverse.com!