The issue is that the SQLExpress install fails as the systems thinks there are pending file deletes to happen during a reboot, but even after the reboot you get the same error.
The below is the error that is seen.
The registry key that needs to be updated is under:
HKLM > SYSTEM > ControlSet001 > Control > Session Manager > PendingFileRenameOperations
Just open the entry and delete the contents, close the Lync Deployment Wizard and re-run the Lync Bootstrapper. All should be good.