Due to a problem with the Intel® Quartus® Prime Pro Edtion Software version 18.0 and earlier, you might see this problem. When any of the last 4 Kb of configuration bitstream 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 has been fixed since Intel® Quartus® Prime Pro Software version 18.1.