All ISP, JTAG. IAP can be used to program after enabling a secure boot. but you must use it program signed image, otherwise, it can't pass the secure boot check.
It's not possible to program the flash with IDE debug because it's not a signed image when debugging code.
AN12283 LPC55Sxx Secure Boot
AN13037 LPC55Sxx Debug Authentication
Maybe that app note could help you.
Best regards,
Pavel