I have read that it takes a long time for the Links to Your Site in GWT to update. But it has been several months. Here is the situation.
Some history, feel free to skip this paragraph.
The site that I want to restore Google ranking to has been online since 2000. It performed #1 result for my terms from then until around 2007. With new competition and continuous google changes and a few mistakes and hard lessons learned, I still maintained results within the first three pages after 2007. The site went through a few revisions, from straight up HTML, to e107 to wordpress (current). Really positive results started to occur over the summer this year (1st and second page rankings for competitive terms). Started to feel like the old days again.
Then I was hit with an algorithmic change on Sep 28 or thereabouts. Dropped well out of the first 30 pages if not more for just about everything minus my homepage site title and a couple well linked pages.
I have gone over everything with a fine toothed comb, made plenty of quality changes and I always come back to what I suspected was the problem from the start. One of my other websites (Site B) was linking to two or three pages on the problem site (A), and these links were at the top of every page of Site B. Site B performs very well in Google, #1 for the terms I want, and generally high for relevant other terms. But GWT was reporting 800,000 links from Site B to Site A. I hadn't been paying attention to SEO so much until the traffic drop, but when I saw the information about sitewide links, over optimization, etc, I immediately removed the links at the top of Site B.
It has been since the end of September, and now there are about 460,000 links still being reported. Of course in reality there are currently ZERO since that time.
I experimented with some other links at the top of Site B. I linked to some newer HTML sites I have that really didn't have much significance in google. At first they showed strong results in google but then faded away after a few days. I removed the links and then they return really strong in google, and these are pretty new sites. One is a year old and the other only a couple months. They have a handful of other IBLs which help, but Site A has a pretty strong link profile and solid content. So when Site B produces 800,000 sitewide links I can see how that's an obvious problem and my experiments confirmed that.
I believe this is the source of my problem. I just want to know how much longer I can expect to wait for this report to reflect reality and if there is any way to expedite the update.