Description
Due to a problem in Quartus® II software versions 12.0 and later, you may see this warning message when archiving your design regardless of whether you have previously compiled or run Analysis & Elaboration on your project.
Resolution
If you have previously compiled or run Analysis & Elaboration on your project, you may select No to proceed with project archiving. Otherwise, you may select Yes if you want to run Analysis & Elaboration before archiving your project.
This problem is fixed beginning with the Quartus II software version 12.1.