I don't think it'll screw up your boot0, boot1, and boot2... Your System Menu is loaded at IOS60, 30, 70, 20, 10, etc. I don't know how it would screw it if the System is being loaded at IOS60. The boot0, 1, 2 are loaded once. Unless it was a hard reset.
Oh and I just realized that SD Menu is gone. With WiiConnect24 and Country.
Is it a "safe mode"?