The only way I was able to update the flashbios is through config live. If I'm reading your post correctly you are not able to get into config live? The other way is to set your dip switches for a single 256k bank and to flash that via http. This willl not touch your backup flashbios however. If you are trying to use this to get your flash to work however you may be in for more trouble as that is most likely not your issue.
Make sure that all the flash protect switches are disabled on your chip and the external switch. It would make it easier just to remove the external switch while testing to make sure the external switch is not the problem. Try flashing like that an see if you have any more luck.
If you do you can ftp your updated flashbios to the hd on the xbox and use config live to flash your backup from within bios tools.