Due to a problem with Intel® Quartus® Prime Pro Edition software version 19.3 and later, reconfiguration of IOPLL IP with the IOPLL Reconfig Intel® Stratix® 10 FPGA IP may fail to work correctly when using Intel® Stratix® 10 devices. You may find that, after a reconfiguration request, the IOPLL does not get reconfigured.
To work around this, compile your design using an IOPLL IP file from Intel Quartus Prime Pro Edition software version 19.2.
This problem is fixed starting from Intel Quartus Prime Pro Edition software version 20.4.