I have an indexer which is also being used as a search head. It was Splunk version 6.0 and all the data was showing in the dashboard, but when I upgraded it to 6.3.2 , no data is showing up. Even If I forward any new input from the forwarder, it is not showing up in the "Indexer".
I don't know of any issue with data disappearing when upgrading to version 6.3.2. Have you tested that the searches you use in your panels actually work? That is, if you click "open in search" on one of your panels, do you get any results?