Should I disavow these links?

To disavow or nofollow or something else?

[Allreaders]

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]

[mademetop]

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.

[n0tSEO]

Webmaster Tools is a bit slow at updating links, so don't worry about it if you have already fixed the problem. ;)