You can download the LPC9xx bootloaders from a link on the Flash Magic web page. See the third party section towards the bottom.
Flash Magic provides the protect ISP option. A parallel programmer should not.
If you are running into problems using Flash Magic and devices failing to work after being programmed with the protect ISP option turned on, then we can investigate that further. However if you are programming with a parallel programmer then you can do anything, including erase the bootloader.