RTF is a global modification that replaces all towns in the game.

I'm trying to understand why the polygons are disappearing. Notice that they disappear only in certain areas – the mouth, nostrils, ears, and eyes. I tried highlighting the areas by edge length in Blender, and the selection looks similar to the invisible polygons in the editor. Perhaps something like this is affecting the disappearance – "very small edge length, small polygon, relative size, or absolute size."
Here's a comparison in the picture with arrows. I moved the edges slightly in that area, and the hole became smaller.
Then, I decided to try an experiment. In the second picture, I used a brush in Blender to, hmm, increase the distance between the edges in the left corner of the mouth and the nostril. The result was completely unexpected: the right nostril became almost entirely visible, the left corner of the mouth is now more transparent, and there seem to be fewer holes in the ears.