I moved the CAD model into the root folder of your project so it is co-located with the Windchill Part. I did not remove either. I'm sure if you collected the Windchill Parts as part of the removal process or just checkmark both, you should be okay.
For FIRST, I would strongly recommend againast creating Windchill Parts to go with your CAD models. It is just going to add a layer of confusion you won't want to deal with since PDM is not available.