whatson - 9:51 pm on Jun 2, 2011 (gmt 0)
404 the pages, and eventually they will drop out of the index. However, some people are reporting in further losses in rankings when dropping so many pages of their site. I am guessing this might be something to do with PR, i.e. the PR has been spread to all the extra pages, but when they go down they are no longer able to feed the PR back into the site. I am guessing you just need to wait for a big re-indexing update from Google until all is well again.