I had two sites,which linked to each other. Recently I became aware that it was bad to have thousands of links from one site to the other, so I folded all the content into one site and made the other site's pages all 301 redirects (to pass pagerank to the primary site).
However, my webmaster tools still shows 100,000+ links between the two sites. Should I disavow (and or nofollow) those links, or should I not be concerned?
I have no manual actions listed.
[edited by: mademetop at 12:21 pm (utc) on Apr 1, 2014] [edit reason] No specifics or URLs please [/edit]
Cross linking is always inherently bad! However, you appear to have done the correct thing in taking away this problem.
I assume you have already removed the links to the non-existent site from the one you have updated in which case the links should eventually fall from being considered by search engines with nothing more needed from you - apart from a possible reconsideration if you have already received a penalty from search engines.