Due to a problem in the Intel® Quartus® Prime Pro Edition Software v20.4, the Intel Agilex® SoC device may fail to do HPS cold reset when you execute the reset command in uboot or reboot command in Linux if the FPGA configuration first mode is used in the design.
To work around this problem, download and install the following patch 0.03 for Intel® Quartus® Prime Pro Edition Software v20.4:
This problem is scheduled to be fixed in a future version of the Intel® Quartus® Prime Pro Edition Software.