Due to a problem of Intel Quartus® Prime Pro software version 18.0 and earlier, you may see this problem. When any of the last 4kB of configuration bitsteam is corrupted, Intel Stratix 10 devices can enter user mode with CONF_DONE pin and INIT_DONE pin being high and the user function works. But the subsequent reconfiguration will fail.
To recover from this reconfiguration failure, power cycle the device and ensure the device is configured with a good bitstream.
This issue will be fixed in the future version of the Intel Quartus Prime Pro software.