The history will be retained.
When SharePoint cleans up workflow history after 60 days, it does not actually delete items from the history list. It just removes the association between the SharePoint workflow history page and the list item. Also, the workflow status column will change to empty.
When you go to the Nintex workflow history page (from the 'view workflow history' link in the menu item), and click through to the text view, there are three sections:
Action log and Task information is taken from our database, and the Message section is taken from the history list. We do not automatically purge data from the database, and as SharePoint doesn't actually remove items from the history list after 60 days, all the data will remain.