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But there's one consolation in the chaos: these reports are just that - reports. That is, they do not directly represent the full data set that is currently powering the ranking calculations, and Google never promised us that that kind of report.
The Webmaster Tools reports are usually more in-depth than the publicly available link: operator results. This means that only a validated owner can see the fuller list, but even that list is still incomplete compared to all the link data Google has gathered.
My sitemaps are currently reporting zero urls in them and then the next day they report correct.
An index sitemap (one that just links to the other sitemaps) is reporting the full amount of urls on the site.
So, I tend to think that Google is working on some changes and not all reporting is correct, IMHO.
And as Ted says, they are just reports and we have no idea when/how they are updated.
The reason: my main domain with all subdomain is since 27th October filtered.
I think this is because in the year 2000, I made one of the subdomains as central for all cgi services. Mainly forms.
Each page hat a contact link to a form on this subdomain.
The service page builts up the complete navigation of the calling site, only the content is replaced by the form to fill and send.
So it looked like this subdomain has with about 10.000 pages about 300.000 links to all my clients domains.
I removed this comlete begining December.
I think the filtering will stop, when all this links disappear.
But when I look in webmaster tools on client domains, there are at external links still all this links from this subdomain, mostly dated last discovered in November 2007.
As with every other piece of Google info, best to use it as a guide only and continue to try to add value with great content, good on-page SEO and lots of effort to get the great quality links.
Yahoo's link data is MUCH worse!