Near disaster averted after flashing rom within Windows!

Other day was updating my bios for an old MSI X99A bios rom to the latest beta version MSI had released. Was lazy that day and decided to use FPTW64 which I have used 100 times before especially on that motherboard.
After ‘FPTW64 -F nameofrom.A1’ with administrative priveledges I get a bunch of ‘Sequencing sector errors’ and can not write to block whatever. Also ran Meinfowin64 and got a bunch of errors. Now my rom bios could very
well be corrupt and I knew trying to reboot could cause issues. So I download a fresh copy of FPTW64 from the 9.1 r7 kit and tried again. This time it completed without errors though less sectors were written to so still worried.

So restarted windows and wouldn’t you know it got stuck at post code 99 or 98 or something. I nearly felt sick and panic nearly set in. This happened two times. On the third try was able to get into bios menu believe it or not
but the system displayed video card pci-e post information on the screen I never saw before. But I was in bios and could now go into QFlash and this time flash it again within the bios rom utility. This was surprisingly quick
but afterwards it booted straight into Windows so I was happy.

The kicker is the board has dual bios so I worried for nothing I guess!