I am experiencing a problem where linked file XXXX.rvt cannot be saved because it has changes in more than just shared coordinated and therefore can invalidate local files owned by you?
This error will occur if your linked RVT file contains a linked DWG file (or other CAD file), and that DWG file has been changed on disk since the last time the linked RVT file was saved. When you load the RVT file as a link, the DWG file is reloaded and Revit detects that it has been modified. As long as you will not be making any changes related to the shared coordinates, this error message is not relevant and you can ignore it. However, if you are making changes related to shared coordinates—including moving an RVT link that uses shared coordinates—these changes will not be saved. As a workaround, you can open the linked RVT file referred to in the error message, save the file, and then close it. Doing so will update the DWG links contained in the RVT file. Of course, the message will reappear if the DWG file is modified again, until you resave the RVT link.