1) _id index is mendatory and created automatically. So is there any scenario where index got removed
Hi,
Generally the warning message(s) above is triggered on a replica set member restart. A startup check process would discover that some collections exist without _id
index, which would then reset the Initial Sync process.
A possible scenario is when a replica set member was terminated during the synchronisation of the oplog but before the index building stage.
if index got removed then it should synced in secondary too.
It is likely that the primary would have been vetoed and a new primary would have been elected. You should analyse your replica set members logs to get a better picture of the events.
Also I would recommend to use the latest stable release of MongoDB for bug fixes and enhancements. For MongoDB v3.2.x currently it is v3.2.16. See also Upgrade to the latest revision of MongoDB.
Regards,
Wan.