the fact that you may have gotten unfair value for many years is a major positive value at the expense of your competitors.
Think how your competitors feel getting screwed only by Google ignoring your unfair advantage for so long.
This I really doubt, these links value where 0 or hardly 0 on google, remember perfectly all the discussions about them and the impossibility for webmasters to delete them, we are talking about more than 11 years ago. If something I better think if did anything to site I think more harm than a positive value. Before it was easy to see backlinks in google search and I ever seen them as backlinks, in yahoo I did see them and yahoo penalizaed to start with, then started to just ignore them, as they have a common pattern, and are easy to recognize.
Anyway I will do what you say. I just dont feel comfortable with those links. They arent that many though as many disappeared after so many years, and I deleted myself very quickly when I found out how it worked, but the harm was done.