As clearly stated by jeanlain, you only need to have the GTX 680 card in the machine for flashing purpose, so I'm not sure what power issue needs to be resolved? Anyone who has done it before knows it only needs one video card, the one that needs to be flashed. The only reason to have two video cards in a machine is when you need to flash a dead video card, and hopefully this would never happen to anyone.
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Since MSI has more than one GTX 680 2GB model, could you let us know which model number did you flash so people could have another choice other than the EVGA models? Thanks.