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gg.anands@gmail.com, it appears that you config servers are not in sync, and you'll need to fix that manually.
MongoDB 3.2 introduces Config Servers as Replica Sets, that prevents this scenario. You can upgrade with downtime via this procedure. To upgrade without downtime you'll need to use version 3.2.4, scheduled for release next week (you can download the 3.2.4-rc0 release candidate today, which will provide seamless upgrade to 3.2.4). For the upgrade process to work you must get your config servers in sync first though.
Please note that the SERVER project is for reporting bugs or feature suggestions for the MongoDB server. For MongoDB-related support discussion please post on the mongodb-user group or Stack Overflow with the mongodb tag, where your question will reach a larger audience. See also our Technical Support page for additional support resources.
Regards,
Ramón.
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