We recently were notified about unnatural links from two websites (totalling a few thousands links each). We went to the websites and asked them to remove the links, which they apparently did.
After this we applied for reconsideration to Google, explaining the situation, however they came back and said we still have links. We noticed there were still links, however there were less than before, and so we once again asked the sites to remove all the links.
Now we are sure all the links are gone as when we click a random link and view the page source there is no reference to our site, however WebMaster tools is not updating the link list, claiming we still have thousands of links.
Do we have to apply for another reconsideration request to get them to re-crawl the sites to get rid of the links, or should it happen automatically?