Due to a problem in the Intel® Quartus® Prime Pro Edition software version 19.2, in a single SYSREF generation subclass 1 system, the JESD204C IP will not enter the user phase due to it waiting for csr_sysref_singledet deassertion.
To work around this do the folowing :
1. After SYSREF pulse generation, assert csr_cgs_bypass_sysref to enter user phase manually.
2. Send another SYSREF pulse
This problem is scheduled to be fixed in future release of the Intel® Quartus® Prime Pro Edition software.