I often flash my BIOS from the HD!
I boot to DOS using a WIN9x bootdisk and cd to the BIOS directory and do it from there! I don't really care that other TSRs are present! It works fine!! After the initial bootup from floppy, it's faster from the HD to flash it! Also when I back up the older BIOS, it saves it to that current directory!!
Good luck bud,
Edblor