To verify the contents of flash after programming, use the standard Serial Wire Debug (SWD) Arm® CoreSight™ Debug Access Port (DAP) protocol to read every address written and compare to expected values.
It is possible that the HEX file being programmed will enable access port (read-back) protection that makes it impossible to verify the contents of flash. This protection takes effect only after a reset is applied. Make sure not to reset between Programming the application core and verifying.