We had an issue going from Lync 2010 to Lync 2013 in our demo environment. Even it said the replication was ok and the database was ok, it did not replicated and we had a Yellow triangle in Lync Controlpanel on the fronend server.
Some work back and forward and we had do uninstall the Lync2013 frontend and install it again.
The do an install of the databases (install-csdatabase from powershell).
Then it worked again......Just a tip on the way.