Yesterday I reported a Google Link Update Within Webmaster Central's Link Tool but I did not dig deeper.
Vanessa Fox of Google Webmaster Central left a comment explaining that this is just an update in the number of links reported. The linkage details, the actual links in the reports, have yet not updated, but will be updated in the next few days.
We are indeed updating links data. So you should start to see updated counts listings soon. In the cases where webmasters are seeing updated counts and not updated listings, they should see the updated listings within the next day or so.
DigitalPoint Forums picked up on the discrepancy between the count of links reported and the number of actual links in the reports. So hang tight, it is coming shortly.