Most Bootloader I know, will ignore the config fuses in your code as they're already set in their firmware and don't have the ability to re-program them on the fly. HOWEVER, for many PIC18, you can do it later in your code. Darrel Already post something on that... BUT, using this, you will probably screw up most Bootloader... no free lunch

Bootloader are nice for firmware upgrade, but for development, they have their own limitations.