As far as I know, CF Flasher still does not support flashing the M52259DEMO board and is it only possible to flash new code using Codewarrior. This is not always the most convenient way though.
Will CF Flasher ever provide support for the M52259DEMO board?
I asked my FAE the same question but he could not give an answer. He did suggest using the MCF52233 selection in the CFFlasher to program the "59.
It has worked but I don't know what would happen if the code was larger than the '33 code space.