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Whenever I try and sync with either emplode or jemplode, then it gets about a third of the way through, and then hangs.

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I think this could be down to my hard drive cable, which has been causing some interesting symptoms of late.

That could be part of it. Again, the FAQ clearly says to solve all your hardware problems first before messing with the file system...

While you wait for the cable from Stu, then go ahead and perform the steps listed. I know that you don't see any files there, go ahead and do exactly what the steps say. It even tells you you'll get error messages for some of the steps, that's OK.