I have had to re-install windows a long time ago after a bios flash but havent heard of anything bad happening recently.
The new BIOS can cause redetection of some hardware which can stall a boot if a critical component gets stuck on boot.
It shouldnt happen now, give it a try.
If you save a copy of your old BIOS and keep a boot floppy handy with the flash util and bios, you can blow the old BIOS back if it goes pear shaped.