Punished by Google - why???

I used to have a great number of encyclopedic articles that were high on [login to view URL] - from 2-5th position. Many are now removed, others are there still. I see no fraudulent additions to the punished articles, they come from the same publishing system as those indexed. This task is simply to identify what has gone wrong, and make clear suggestions to what can be done to solve things. There is one potential cause: I have changed domain name for the very same website two times (over 10 years), causing there to be three effective domains producing the same content. This is a situation that cannot be changed - there are links to my web pages using either three. I have informed Google about this, they haven't minded before. I have also submitted sitemaps...