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I found the solution for this one. It was nothing to do with the LDAP re-indexing.
Recently I defined the Access-Server-Clusters and assigned it to all the existing webgate. I removed the individual AccessServer association available from each webgate after associating to the cluster. I did it from PolicyManager admin screens. That cluster to webgate association process wiped out the existing Access-Server value from respective webgate.lst file (loacated at ..\NetPoint\WebGate\access\oblix\apps\webgate). so the webgate was not able to find any AccessServer to connect. I manually added existing access server value in webgate.lst and now I am able to access the /identity/oblix .