Thanks for the feedback, Toby C.
First of all, I do not have access to Element3D, but I checked a while ago a longer tutorial about. (I found [BTW] a good example of why a depth path shouldn’t be Anti Aliased in it, which I teach since a decade, but now it is even more important than ever :o)
Having admit my limited access about it, I can’t test things here, which I would like—to give a better answer. So I have to guess. Is the Polygon selection, and with that the “Material Selection” done in C4D, working in this plug in?
If so, why not go ahead and merge the many parts of the wheel to a single object? This would simplify the work anyway. Perhaps a merge and bake to a single texture will help to degrease the render time as a nice side effect (If you optimize the final object—which means, delete invisible polygons, merge points etc).
In that way you would have only one object to prepare (I assume all four wheels are the same (You mentioned duplicate)}. If you load in more objects into Ae which have to move in sync, you have to connect the animation for each single part, if I got you correctly, parenting is not an option. I’m not certain what makes work, to prepare the object one time and optimize it even, or, to just load it in after only centering the axis and do anything later on. Again, I’m not familiar with this product in detail. A clean and simple to load model will save time as well as for future projects. Just my two cents.
All the best
Sassi