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Originally Posted by Richard M
Wait for a week and if they're still missing then let me know so I can do some digging. 
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Well it seems to have found my site again and, thank the gods the links are coming up again now, but it was *extremely* worrying...!
Interestingly apparently one thing the latest version is doing is scanning dynamic pages, but because of the way the cart works, each scan comes up with a different reference, meaning that it looks like you're trying to scam multiple hits and thus get penalised! (This wasn't what happened to me when they vanished, because my links were *nowhere* even when I went right to the bottom of the list)
The fix is to modify robots.txt to deny access to the /cgi-bin folder (or similar) so it can't follow links into there.