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Anyway, I solved the problem. The source of the problem is the triangulation process: https://blender.stackexchange.com/questions/7033/how-can-i-triangulate-a-mesh-without-changing-the-object
I solved this by adding and applying a triangluation modifier myself, then applying my normal modification, and then writing my own SMD exporter which expects triangles. The custom normals don't get touched and everything is fine. People who want to use this technique should make sure to save backups of their .blend files without the triangulation modifier applied.
Here is the plugin I wrote: http://pastebin.com/0mfyv4yn
I'm pretty sure they will survive export to SMD too, but triangulation may indeed be an issue. The custom normals system just doesn't support topological changes. :(