This is a pain in the butt to do. In order to unregistered a version with an archive, you need deattach the archive from the feature class. ESRI does not provide any tools to reattach afterwards. You will have to start with a fresh archive at that point. As for the replica, I believe if you rebuild a replica it will use the current archive history and not the previous history.
However, because that would not work for us, I wrote a tool that will reattach (well, copies the records into a new archive). Check out these posts for info on this topic:
Archive Restore Tool
Approach for Data Model Changes
https://community.esri.com/ideas/13248