I've flashed in windows multiple times. About the only thing that can mess it up is a power outage or a persons own stupidity XD (i.e. kicking the off button or triping over your power cord or hitting cancel)
I wanted to do it the old floppy way but my BIOS wouldn't fit on a conventional floppy lol too much work doing it on cd and didnt feel like buying a thumb/usb drive just to flash the bios.
bios updates can add lots of fun stuff. hardware compatability, increased overclocking ability possibly, increased stability..
but the safest way is the old fashioned way: BIOS Flashing, What is BIOS or CMOS flashing?
read that, love it, have its children.
but like i said flashing in windows only fails if the user is a tool or if one of the gods deem you unworthy and cut the power. Or you use the asus EZflash. lol