Some data lost after cluster restart

ES Version 2.1.1

Previous state - A cluster with 6 nodes (3 Master cum data nodes, 3 client nodes).
Index has data for two months (1st April 2016 to 31st May 2016.) Actually, everyday, previous day's data is added and two months old data is deleted.
I restarted the cluster. All of a sudden, 90% of data for the date range 5th May 2016 to 31st May 2016 is gone (average record for these days goes down from 100000 per day to 10000 per day) and, surprisingly, deleted data fro date range 5th March 2016 to 31st March 2016 reappears.

What's the problem?

Do you have any relevant information in the logs?

Did you let the entire cluster complete its restart?