Let's just avoid any advanced modding techniques, please.))
I've encountered this problem before; sometimes, small polygons really do disappear. I honestly don't know what causes it, but I know how to fix it. Just export the model at a larger scale (by increasing the root bone).
The animations will still keep the model at the scale you need (it will be as if it's being scaled down), but the polygons will now import correctly because the game (or the plugin) won't consider them too small.
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And regarding advanced modding... well, you're not far from the truth – no one could suggest a solution to this problem before you.
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P.S. By the way, there was a lot of debate about the NUMBER of polygons per model, saying that the game is old and can't handle many. I tried a test: I took a cyclops from the game, added tessellation in 3ds Max, and the number of polygons became about 300,000. The export in the editor failed. Then I tried, I think, 20,000 (no less), and the editor was able to process the model and display it in the window.