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Mid 2012 MBP with OEM hard drive. I booted it this morning to a flashing question mark folder. I happened to have an external drive with OSX on it, booted to that external drive just fine. I opened disk utilities with the original hdd still inside the MBP, it wasn't listed in Disk Utility, couldn't find it in Terminal.

I popped the original hard drive out of the MBP, booted off the external drive to OS X, connected the original hard drive to a SATA-USB to the MBP, OS X could see it just fine. I ran a disk repair from Disk Utility, everything checked out, said it repaired a few errors, etc. Popped it back into the internal SATA connection in the MBP, and restarted the laptop (unplugged the external hdd). Flashing question mark folder appeared again.

Happened to have a second 2.5" internal hdd with OS X installed. Popped it into the internal SATA connection in the MBP to test perhaps a bad SATA cable, etc. That hdd worked just fine, booted OS X.

I tried resetting the NVRAM (command+option+P+R). I've basically tried everything I could think of, not sure why it's not booting the original hdd. Again, I booted off a different drive and the original internal drive plugged in via SATA-USB, I am able to view the contents of the drive just fine (naturally backed up all my data as I assumed the disk is failing).

Any thoughts, tests, concepts, theories, are all very much welcomed and appreciated!

UPDATE

I've since decided to unseat the internal sata cable and reseat the cable. Upon booting with the original drive, everything booted fine. After a several hours of use, and restarting, the drive wasn't recognized. I have reason to believe the SATA cable is bad. My question now, is there a way to tell if the cable is going bad or if perhaps its a logic board issue? If I'm able to boot external drives just fine, would that imply the logic board is operating normally? Or are we somehow bypassing that function by the nature of being external?

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    As to the edit, I would start replacing components in the easiest / cheapest manner until you've isolated the issue. Keep in mind, each time you flex a cable and reconnect things on the logic board end - you will eventually damage things. The SATA connector on the drive is rated for hundreds of cycles. Some cables and logic board connectors can fail after 10 or even fewer bends / drops / reconnections. (also - feel free to answer this if/when you nail down what was the error. the process and answers that help you get there are all visible and help others in a similar place)
    – bmike ♦
    Commented Mar 13, 2014 at 17:59

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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.

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