When a project has been copied with the compiled database (qdb), you might see that files opened from the Project Navigator are from the original project that was copied. This problem occurs when the project has not been recompiled. The Project Navigator uses absolute paths created during Analysis and Elaboration, which will still point to the original project that you have copied.
This problem occurs in the Intel® Quartus® Prime Pro Edition Software version 19.1 and earlier.
To work around this problem, rerun Analysis & Elaboration on the copied project.
This problem is fixed starting with the Intel® Quartus® Prime Pro Edition Software version 20.1.