AutoCad :: Drawings With Transparency To Adobe (both PDF And InDesign)

For presentations I usually print my AutoCAD files to pdf and then import those into InDesign - worked well enough, but I had not had the transparency function in AutoCAD turned on, so the drawings lacked that feature. Now I'm saving with the transparency setting on in AutoCAD. My test prints of the straight pdf files do work, but they take a l-o-n-g time to print. Am worried that when I import them into InDesign it will slow down that process as well (I recently had one drawing that inexplicably hung up at the plotter all together and wonder now if transparency from an imported file was the problem). I don't need to keep the transparency live through InDesign. What's the best way to set up that import process? Do things need to be flattened, and if so, at what point?

I should amend this by noting that I mean flattening in the graphic design flatten-the-transparency sense, not in the 3d-to-2d CAD sense. All the drawings are 2D......