Had to manually remove certificate entry at
\\computer\HKEY_LOCAL_MACHINE\Software\Microsoft\Microsoft SQL Server\MSSQL11.MSSQLSERvER\MSSQLServer\SuperSocketNetLib
Clearing certificate settings using Sql Server Configuration Manager turned out to have no effect.
Certificate was failing clustered instance startup.
Hence, seeing instance failing startup after clearing certificate settings using Sql Server Configuration Manager brought about additional check.
After clearing registry entry manually instance started with no issues.
It would be nice if Sql Server Configuration Manager could handle the task.