Take all the bad pages, set up 301 directs on them, and point them to good new pages. Or an easier way, would be to delete them all, and send all requests for unfound pages back to your home page. The first method spreads the word about internal pages, the second is simpler.
You seem to imply that the entire site could be blacklisted. That isn't normally the case, usually just some pages get listed poorly because of something done incorrectly.
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