Earlier this week I had a project where we were moving the back-end Lync database from a standalone SQL to a clustered instance (pilot to production for Enterprise Voice!), but we ran into an error I haven't hit before when trying to add the new SQL store to the topology - Topology Builder was failing on the enabling topology step with the error "The directory name is invalid." As a result the databases and permissions were not even being populated in the new instance.
We checked the usual suspects: firewalls, permissions, etc with no luck. In the end we just used a different machine that had Topology Builder installed and the same topology file published OK. After doing some more research it seems this is a very generic SQL error that can typically be resolved with a reboot (of the server trying to talk to the SQL instance). So if you hit this error I would suggest just using a different machine, or restart the one you're using.