Hi @jenandesign,
May I ask you which version of Cinema 4D are you using?
So typically the issue with Polygon Reduction is the same as the one from Python plugin(Python Generator?). Are they the only affected objects types or all generators are affected?
In any case, FBX format has no knowledge of what is Polygon Reduction/Python Generator so he has to bake it as polygon Object.
But for doing that it needs a proper cache representation of these generators. And since you Load the file in memory the scene is not yet evaluated (and cache not built).
So please call BaseDocument.ExecutePasses to build the cache.
For more information see related topic Cloner objects missing in Commandline FBX export.
Cheers,
Maxime.