http://compare.buyhatke.com got hit by the recent algorithmic updates. What I could find out as of now is that I have 3-4 services hosted on different subdomains and we keep a constant navigation bar at the top for all our subdomains so that a user can switch easily between services.
Now the problem is the services are not completely related to each other and due to lots of pages on our websites. The count of backlinks as shown in Google Webmaster Tools has also increased to 109,857,360 which is very large.
So can the backlinks be the culprit given that they belong to different subdomains, and Google might consider them as spammy links, while in reality they are just to simplify navigation, and to keep displaying the top products from each service in the navigation bar?
Should I remove the backlinks by using Disavow tool?
Should I use a nofollow tag in all the URLs of my navigation?
What would be the best way to clean up this?