A site with solid indexing and significant traffic was sculpted with nofollow several years ago. What the owner did was add nofollow to every link in the sidebar of every page, EXCEPT the index page, while placing important links in the header and interlinking pages via use of "related content" links.
The result was intended to be link value passes through the header links sitewide, it passes from article to related article with the related content links and minimal value passes to the category links in the sidebar (linked without nofollow only from the index page).
It worked and I have a feeling the site may be grandfathered in some way with it's current layout.
Fast forward to now, post Matt Cutts proclaiming nofollow doesn't work like it used to, and the owner wants to make changes. Analytics shows the hotspots to be the prominent header links and to a lesser extent the similar article bottom links while only 0.4% click a sidebar link.
With the above scenario...
~ would completely removing the currently nofollowed sidebar links from every page except the index, perhaps replacing them with advertising, increase the pagerank value passed through the other links? (this would cause an instant 60% fewer internal links per page, all of them previously nofollow)
~ would such a drastic change cause search engines to simply ignore the change and prevent the content from moving up or down in rank using whatever it is they do?
~ would it cause other complications?
What would you do ?
