ID:138082 Current release of the Quartus Prime software does not support Incremental Compilation and Rapid Recompile simultaneously.
CAUSE: The current release of the Quartus Prime software does not support using both Incremental Compilation and Rapid Recompile at the same time.
ACTION: Perform only Rapid Recompile or Incremental Compilation. To perform Rapid Recompile, remove the Incremental Compilation partitions. To perform Incremental Compilation, disable Rapid Recompile.