If you are trying to replace a PDF file that is already under Calibre control then you can do one of two things:
- Replace directly the file that is already in the Calibre library taking care that you do not change the filename. This will work although it is not the recommended method.
- In the Edit Metadata dialog add a file that is NOT under Calibre control using either drag-and-drop to the Formats window or via one of the Add buttons. This is the recommended way to do things.
What you must
NOT do (and I think you are trying to do) is to try and combine these methods and use the second of the above options to try and add again the file that is already under Calibre control. This will go wrong because Calibre always takes a copy when adding a file and this results in calibre trying to copy the file to itself.