I had to put this project aside for a while, just picked it up again couple days ago.
Its true that the LPC2000 has a command line interface as mentioned by @RTSLVU but I couldnt locate any related documentation. Not sure if the program streams the result of the programming to a file (again, no documentation), but the program returns no status message at all to the command line. This means I can only know if the program has finished the execution but no idea if it was successful or not.
Found an alternative called Flashmagic, which seems to work just fine and has proper documentaiton.