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Hi Moz Community! We have a client in the manufacturing industry that is listed in Thomasnet.com for a about 75 different terms. For those that might not know, this is a paid directory site that ranks extremely well and has a very high DA at just under 90. These 75 different terms have spanned about 9,000 "dofollow" links on Thomasnet.com around 4 months back, right about the same time as the Penguin 2.0 update. The link profile for this client had around 2,000 links prior to the 9,000 additional links, and our team is unclear if we should be concerned about these paid directory links. The organic rankings have dropped a bit, but that might be because of a more general Penguin update and not be directly tied to this paid directory. I'm looking for some general guidance and recommendations in this paid directory space and help with Thomasnet.com if available. Should these links be requested as changed to "nofollow"?
Will Google see this domain as one major domain link?
What other recommendations/experience with "quality" paid directories can be expected? Thanks much and look forward to your comments and discussion. Dario

About 9 months back we thought having an extremely reputable company build our client some local citations would be a good idea. You definitely know this citation company, but I'll leave names out. Regardless, it's our mistake to cut corners. Google Webmaster Tools quickly picked up these new citations and added them to the links section. One of these citation spawned a complete mess of about 60K+ links on their network of sites through ridiculous subdomains of every state in the country and so many other domain variations. We immediately went into remove mode and had the site's webmaster take down the bad links from their site. This process took about a month for outreach. The bad links (60K+) have not been on the spam site for well over 6 months but GWT still shows them in the "links to your site" section. Majestic, Bing, and OSE only displayed the bad links for a brief time. Why is webmaster tools still showing these links after 6+ months? We typically see GWT update about every 2 weeks, a month tops. Any ideas? Could a changed robots.txt on the bad site prevent Google from updating the links displayed in GWT? We have submitted to disavow, but Google replied with "no manual penalty". We even blasted the bad site with Fiverr links, in hopes that Google would re-crawl them. No luck with anything we do. We have patiently waited for way too long. The rankings for this site got crushed on Google after these citations. How do we fix this? Should we worry about this? Any advice would really help. Thanks so much in advance.