Intel® Stratix® 10 device will fail in subsequent reconfiguration after JIC programming if you are using SFL (Serial Flash Loader) helper image (Factory default SFL image).
Use one of the following workarounds in order to perform reconfiguration after JIC programming:
1. If the Intel Stratix 10 device is configured, you can uncheck the SFL helper image configuration and continue with only the JIC programming.
2. If the Intel Stratix 10 device is unconfigured, power cycle the device after the SFL helper image configuration and JIC programming.
This issue will be fixed in the future release of Intel® Quartus® Prime Software.