Mid-2012 MacBook Pro hard drive failure (maybe? not really.)
Since only one drive gives you a flashing ? when mounted internally, you've pretty much ruled out hardware failure of the controller and the cabling. 

I would first try booting into the start up manager by holding the option key with the problematic drive on the internal bus. The ? can come up when the startup disk settings in NVRAM don't match the drive, but if any drive connected is bootable, it should show when you boot with option held down. 

Your next step after making sure it's not startup disk settings would be to erase that drive entirely and try reinstalling OS X onto it. You could flip a coin and decide to do the installation internally or externally.