Hi,
there is a GUI and command line version of Pemicro flash programming utility available as a part of CodeWarrior for MPC55xx v2.x
GUI:
c:\Freescale\CW for MPC55xx and MPC56xx 2.10\pemicro\cw_progppcnexus.exe
Command Line:
c:\Freescale\CW for MPC55xx and MPC56xx 2.10\pemicro\cw_cprogppcnexus.exe
This way you can write your own script and execute it. User Guide is attached.
Hope it helps.
Stan