Hi,
Check this link https://www.intel.com/content/www/us/en/docs/programmable/683786/current/how-real-time-isp-works.html, In real-time ISP mode, the user flash memory (UFM), programmable logic, and I/O pins remain operational during the progress of the CFM programming. After programming is successful, the device waits for a power cycle to occur, and then the CFM contents are downloaded to SRAM as part of a normal power-up sequence. After tCONFIG time, the device enters user mode.
The real-time ISP mode requires the JTAG for CFM programming as well. ISP totally without JTAG is not possible. If you want to use real-time ISP mode, follow the steps in this link https://www.intel.com/content/www/us/en/docs/programmable/683786/current/real-time-isp-with-serial-vector-format.html
Thanks,
Best Regards,
Sheng