Due to a problem in Intel® Quartus® Prime Pro Edition Software version 21.3 and earlier, reconfiguration of Intel® Agilex™ devices may fail if the external host resets the QSPI flash and then toggles the nConfig signal for reconfiguration. In this condition, the SDM firmware does not trigger a QSPI recalibration flow as the SDM is not aware of the QSPI reset event triggered by the external host.
This problem has been fixed in Intel® Quartus® Prime Pro Edition Software version 21.4 and later.