Sometimes external drives have to be "woken up" before they can be accessed. If the backup process craps out, try browsing to the drive in Finder and going deep enough in the folder structure that you notice a stall that lasts a couple seconds, and then try restarting the backup process.
I used to get this issue when I had my music on an exteral drive. If the drive was sleeping when I opened iTunes, it would not find any of my songs. I'd have to close iTunes, wake up the drive as described above, and then reopen iTunes.
Not a solution, I know, but if it works then it will at least tell you what the problem is.
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