Clone no longer sees MBP internal drive

When I boot up from a clone on an external drive, the internal drive of my MBP no longer appears in the Finder -
nor does it appear as a startup disk in System Preferences.
In fact, none of my clones are recognising the MBP any more.
The MBP drive is only 3 months old, and Apple branded, and all drives are formatted OS Extended (Journaled).
Everything was working perfectly until recently - without there being any changes to the setup as far as I know.
Any idea what’s happened, and how to fix it?
It’s a mid-2009 MBP running 10.9.4.
(I originally posted this in the Mavericks forum, but maybe it's even more relevant here.)

Apple does not produce any drives on their own - so any "Apple branded" drive would be manufactured by a third-party.
Have you tried booting into your Recovery partition (hold down the command and R keys whilst booting) and using Disk Utility to Verify and, if needed, Repairing your internal drive? Does your machine boot with all of your clones as well as your internal drive, but does not show up on the Desktop when booted from a clone? Have you used Disk Utility to see if the machine actually 'sees' the internal drive?
Call back,
Clinton
MacBook Pro (15-inch Late 2011), OS X 10.??, 16GB Crucial RAM, Crucial M500 960GB SSD, 27” Apple Thunderbolt Display

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