Yeah, I've got to say that although your idea worked, having dents in the pepakura, especially the UN-RESINED pepakura, is almost a given. Just in the future, this may help you out a bit in that it is a lot less complicated and is fully backed up by the site and other forum posts:
Take the pep piece and support the paper inside however you can (little struts that make the pep less flimsy, like Popsicle sticks of rolled up paper)
Resin the outside, fiberglass the inside
Place bondo on the "dent" or any flat surface for that matter,
Sand the dickens out of it until it is level with the rest of the part and/or sand to the curve you want
I am glad that your method worked, the only thing that I am concerned about is how you tried to fix it while it was still only paper...
You can't exactly trust that whatever you fixed in pep will turn out after resining and fiberglassing, because that sometimes causes small bits to sag or warp (this is minimized by adding supports, like above). But if I can strengthen and round/level a piece in essentially two steps, I am all for it...
I would try this method here, it is the gold standard for nearly all of us Pep workers and is only as complicated as going to Home Depot, Lowes, Walmart, or Costco...
I hope your armor turned out well!