Phoronix: Flashing Your BIOS From The Linux Desktop
Linux hardware support has improved a great deal over the past few years, but there are still a few troubled spots. With computer motherboards, for instance, the core functionality is generally there and most consumer motherboards will "just work" with the latest desktop Linux distributions out there. Where users though can run into problems are with the ancillary features. Motherboard manufacturers usually bundle proprietary software with their products that allow monitoring of hardware sensors, flashing of the motherboard BIOS, and overclocking all from within the Windows operating system. With the exception of LM_Sensors providing some sensors support, this is a grey area for Linux. Fortunately, however, the folks working on the CoreBoot project have developed a program that will near universally allow you to flash your motherboard's BIOS from within the Linux desktop.
Flashing from Windows is totally crap and dangerous, and depends on the company behind the motherboard. If this tool works reliable, this would make things easier for Linux users than for Windows users I'll try it out once the v1.0 release appears.
Hmm. I'm not a big fan of flashing your BIOS while an operating system is running on top of it either. If you have any kind of power management running chances are pretty good that there are occasional calls into the BIOS happening... and if one of those calls happens while the BIOS ROM is blank, that would be a problem.
I wouldn't flash the BIOS under any OS unless I already had a recovery plan - either a disk or a shadow BIOS stored in the flash.