Due to a problem in the Quartus® Prime Software, when the ‘Version-incompatible compilation database files’ file subset option is selected, you may observe this warning message when archiving a project with partitions included.
This warning message can be safely ignored, the compilation database files for the partitions included in the project will be included in the Quartus Archive File (.qar). This problem is scheduled to be fixed in a future release of the Quartus® Prime software.