In the Intel® Quartus® Prime Pro Edition Software version 21.1 and prior, there is a problem with the Intel Agilex® FPGA SDM QSPI controller being disabled for the HPS after the initial FPGA configuration occurs during HPS boot first mode. This occurs after the first FPGA configuration from both U-Boot and/or Linux.
To work around this problem, you can re-probe the QSPI flash driver after the initial FPGA configuration.
To re-probe in U-Boot, run this commmand:
SOCFPGA_AGILEX # sf probe
This problem is scheduled to be fixed in a future release of Intel® Quartus® Prime Pro Edition Software.