Find the current flash that is on your motherboard and store it somewhere. Then, if things do not work, you should be ale to flash back to the current BIOS.
Some flashing programs let you save the current BIOS also, but not all of them do that.
If you end up having to re-install Windows, and you do not have another partition or another hard drive, you will lose the data unless you back it up. You should always backup your data even if you are not flashing your BIOS!