How do you " re-release " big sites

How to avoid the flagging and freezing of big sites on re release

[Whitey]

I'm familiar with Matt Cutt's statement on launching big sites and limiting it to around 5000 pages per week. But what do you do if you alter an existing site and find yourself with no pages being indexed or served in SERP's?

For several years we operated a large site of some 500k+ pages.

We ran into duplicate content problems which were fixed in around Aug06. As part of the tidy up process we altered the URL structure and 301'd the old URL's to new ones.

Since Aug06 we have been unable to get more than 450 pages showing on the site:tool

Should we file a re inclusion request? Is there any way to get us out of this "log-jam"?