two things
1- It should never need to happen, since a bootloader's job is very well defined, single-purpose, and easy to debug.
2- If it DOES need to happen, for whatever reason, it's easy. Upload a program who's sole job it is to overwrite the bootloader with a new bootloader. As I indicated, you can write and upload code that will clobber the bootloader Flash, just don't. Not like you will accidentally do that, self-programming program Flash is very purposeful, complicated, and dark-magic that is never be necessary for a user app, its only ever done by, well bootloaders. Remember I'm talking about the Flash here, not the on-board EEPROM, use that for whatever you want.