It works slightly different way on MPC5644A (and all MPC55xx) and MPC5604B (and most of 56xx).
Erased shadow flash means in case MPC5644A that device is censored. In case you switch to serial boot mode, you can access to the device over JTAG, but internal flash does not work (it means internal RAM target works, internal FLASH target does not).
In case MPC5604B device, in case shadow flash is erased, device is locked out permanently and neither JTAG access is allowed. Thus the device is broken and there is no other way how to repair it.