Thanks to martinibuster for asking me to update this.
So we lost these links on 6/1, which was a little over a week after the original post. I'd estimated 60-90 days initially until the links went away. We thought we'd have that much time to begin winding down the site, but they wanted to transition at the end of the month so we obliged.
At that time we were ranking #7 for the head of search term which was included in the anchor text but not as an exact match.
Here's a timeline of what's happened since. (My rank checks are reported weekly):
5/27 - homepage ranked #7 for query 6/1 - site goes down, 301ing to our home page
6/2 - homepage ranked #8 for query
6/9 - homepage ranked #6 for query
6/16 - homepage ranked #8 for query
6/23 - homepage disappears from serps (just for this query); interior page ranks #7 for query
6/30 - interior page ranks #7 for query
7/7 - interior page ranks #10 for query; homepage reappears at #15 as well
7/14 - interior page ranks #9 for query; homepage disappears from serps (just for this query)
7/21 - interior page ranks #11; homepage reappears at #12
7/28 - interior page ranks #10; homepage remains at #12
8/4 - homepage ranks #11; interior page ranks #12
8/11 - interior page ranks #10; homepage ranks #14
Looking at keyword visibility in general for many terms I track, nearly 200 have dropped from page 1 to page 2 since the beginning of June.
However, I think it's important to note that the SEO woes I've faced this year are not only limited to losing links from this one high profile site.
This thread [webmasterworld.com
] details issues I've faced with our URLs being manipulated by Google such that the URLs we use in internal site linking, sitemaps, PPC, emails, natural and acquired inbound links, etc. are being discarded by Google in favor of URLs that they create (this is based on poor 404 behavior on our site, along with a lack of canonicals).
Also, we had been on the slide most of the year for this query anyways, beginning the year at #2, then slipping to the bottom of page 1 where we are now.
So to attribute all of this to the loss of these links is not accurate and only part of the picture.
However, I do believe those links going away has had an impact, not only in rankings, but in what is ranking.
The internal page that Google now seems to prefer for this particular head of search query always hovered in the 90s in terms of its ranking for the same term. Just prior to Penguin 2.0, it had risen to the high 40s in rank. (No optimization was done to effect that change.)
Penguin 2.0 launched and it dropped from the serps as part of 2.0's redundant domains tweak until 3 weeks after we lose these links, where it shows up again as the new most-relevant page in Google's eyes.