Due to a known problem in the Intel® Quartus® Prime Standard and Pro Edition Software, programming the csr_cgs_bypass_sysref register bit to '0' when the JESD204B Intel FPGA IP is in ILAS phase will bring the IP back to CGS state. This impacts Intel Agilex®, Intel Stratix® 10, Intel Arria® 10 and Intel Cyclone® 10 GX device families.
To work around this problem, avoid programming the csr_cgs_bypass_sysref register bit when the JESD204B Intel FPGA IP is in ILAS phase. There is no fix planned for this.