Solved
Hi,
There shouldn't be any issue on writing the 2nd half of the flash if it is not overwriting the factory image (if you confirm that it is able to fit within the 1st half of the flash).
You can refer to design example from https://www.intel.com/content/dam/altera-www/global/en_US/uploads/4/4f/Remote_system_upgrade_c10lp_quick_start_guide.pdf