Not on a riser yet...How can I re-flash stock BIOS when ATIwinflash does not even detect it?
I'm going to guess you have both cards installed on the x16 PCI-E slots on your motherboard.
Some things to try, in no particular order.
1) Use ATIflash, the comand line version not the Windows version.
2) Fit the errant card in a different PC and try re-flash it fom there (with Windows 10).
3) Remove the good card an try re-flashing with just the errant card.
4) Use, as suggested, DDU
http://www.guru3d.com/files-details/display-driver-uninstaller-download.html and re-install the video drivers (make sure you select safe mode in DDU).
5) Try the card in a different PCI-E slot all by itself.