In AEM 6.1 we have seen that upon restart of the servers (especially in clustered mode) at times re-indexing gets triggered. If there is lot of data in the system then re-indexing goes on for hours (approx 18 hours for 400 GB data).
Adobe recommends that we set the system property "oak.indexUpdate.failOnMissingIndexProvider" = true
This property has been created to prevent issues in which some bad shutdowns had triggered re-indexing on the property indexes.
Note: Minimum requirement is Oak1.2.13
More details @ https://issues.apache.org/jira/browse/OAK-3505
