if the BIOS manufacturer releases Windows Based BIOS Flashing, then use that, as its the most safest way of flashing.
example->Windows Based BIOS Flashing - Intel DG965WH BIOS
Important Notes:
• Update the BIOS on your computer only if the newer BIOS version specifically solves a problem you have. We do not recommend BIOS updates for computers that do not need it. You can view all new BIOS fixes in the Release Notes.
• If a BIOS update process is interrupted, your computer may not function properly. We recommend the process be done in an environment with a steady power supply (preferably with UPS).