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I'm guessing that the "pagerank not assigned" yet pages are eitehr pages that have gone supplemental because of disappearing, or that the pages remaining just have a higher percentage of new content - did you keep the newer material and lose the old?
These are just guesses - somebody more learned here will be able to tell you more...
One thing is certain...those who have lost ground have also experienced a large increase in "PageRank not yet assigned" in their Google Sitemaps.
Interestingly, when checking site through the errant spider, they're right.....most of my pages don't show a rank yet.
But when going to other data centers, my pages are all ranked.
Yet in the sitemaps, it continues to report a large portion of my pages unrated.
And the plot thickens!