We seem to have hit a wall on this one... For one of our large clients we recently ran through the process of upgrading a 2010 web app from classic to claims authentication in preparation for a migration to SP 2013. It seemed like everything had went as planned until we noticed that nearly ALL Nintex workflows are now showing as unpublished. Upon further investigation it also appears as though list associations have been lost which would certainly explain why we've been unable to start new workflow instances.
I've been scouring the web looking for possible remedies and came across this doc on the community site: Claims based authentication Nintex Workflow 2010 > 2013 migration that lists this issue as one of the many possible side effects. Unfortunately, the steps it outlines did not resolve this issue for us.
Has anyone seen this? If so, aside from republishing all of the workflows, what did you do to successfully solve this issue.