The percolator has been redesigned and because of this the dedicated _percolator index is no longer used by the percolator, but instead the percolator works with a dedicated .percolator type. Read the redesigned percolator blog post for the reasons why the percolator has been redesigned.

Elasticsearch will not delete the _percolator index when upgrading, only the percolate api will not use the queries stored in the _percolator index. In order to use the already stored queries, you can just re-index the queries from the _percolator index into any index under the reserved .percolator type. The format in which the percolate queries were stored has not been changed. So a simple script that does a scan search to retrieve all the percolator queries and then does a bulk request into another index should be sufficient.