1) write a bootloader
2) reserve n pages of the flash (usually at the top) for your bootloader, load those into the flash by JTAG together with the original program.
3)make a /special keysequence/switch on the board/serial input/other means/ jump to the bootloader from the applications program.

program update

1) the first action of the bootloader is to erase all other pages
2) the bootloader then reads and decodes .hex files and stores them into the flash
3) the bootloader exits to the application