AutoCad Reference Manager deleting pipe out of the model

I had an issue where we were cleaning up a set of files to turn in to the client at the end of the project. I used AutoCad's reference manager to fix the paths of all the xrefs to be relative instead of absolute, and a bunch of the models had Cadworx components that were deleted out of the model. I know it is really a problem with AutoCad and not Cadworx, but it seems like it is only affecting the CadWorx components, so I thought I would ask the questions here to see if anyone else had run into this issue.