Ok, if communication isn't the problem. Although one would need to try a new cable to be sure. You got the blue connector to board right?
If so, the I would suspect a power issue. Swap the power connectors on the two drives and see if the other one doesn't appear. The reason why the drive appears after a flash might be an artifact of doing a warm reboot vs. a cold boot????
I really don't see how flashing one drive should make another go missing. But you could flash it back to a stock firmware and see what happens.