I'm kind of confused. Nothing has changed? I was just confirming that I was using the legacy import when I ran into this problem.
Additionally I have found out that my .cproject file is almost 1 MB in size and I think this is causing extremely slow performance when trying to build or close the project settings dialog box.
I'm not really impressed with this import tool because I feel like I'm having to go back and fix things I would expect the import tool to do for me. I think I'm just going to build the project from scratch and see where that puts me.