Hi,
if you want to use Rappid bootloader on MPC5746R, it is necessary to program RBF file to flash memory by JTAG device. Then it is possible to program the flash using Rappid bootloader and serial interface (UART or CAN).
If you don't want to use Rappid bootloader anymore, use JTAG device to erase the flash and then use JTAG device for programming and debugging.
Rappid bootloader is just piece of code at beginning of flash, so it can be erased anytime by JTAG device...
Regards,
Lukas