Is it possible that the shortcut automatically changed somehow, due to File B being a copy of File A?
I have found that it will change if File A and File B have the same name. Here's a test case I just ran.
I created a text document, Memo.txt.
I placed one copy of Memo.txt in a folder on drive D:. In this file I typed, "I'm on D:".
I placed another copy of Memo.txt in a folder on encrypted drive N:. In this file I typed, "I'm on N:"
I created a shortcut to the Memo.txt on N: by right-clicking the file and selecting "Create shortcut". I cut and pasted this shortcut to remove it from the folder on N: and place in the folder on D:. Now the shortcut from N: was now in the same folder as the Memo.txt on D.: I looked at the shortcut properties to insure that the target field still contained the path to the folder on N:. It did.
With N: unlocked and therefore accessible. if I double-clicked the shortcut, and it opened the Memo.txt on N:. I know this because the displayed text file said, "I'm on N:". I then locked the encrypted drive N: by rebooting the machine. This made N: not accessible. I double-clicked the same shortcut, and instead of it opening the Memo.txt on N:, it opened the Memo.txt on D:. I know this because the displayed text file said, "I'm on D:". In addition, I again looked at the properties on the shortcut and the target field now contained the path to the folder on D:. That is, it had been changed by Windows.
I have Windows 8.1 Pro. I know that in Windows XP, if a shortcut's target was moved, Windows would make an attempt to find the new location for the target. I suspect this is still being done in Windows 8. And it doesn't have far to look since a file with the same name as the target resides in the same directory as the shortcut. The difference in this case is that instead of the target being moved, it was simply no longer accessible because the drive it was on was no longer accessible.