We only support rolling multisite upgrades from one minor version to the next. That is, we support 6.3 to 6.4, and 6.4 to 6.5, but not 6.3 to 6.5.
With single version upgrades, the instructions in the documentation should work properly, and they have the advantage of allowing the cluster to return to a complete state more quickly than it would if you were to keep maintenance mode turned on for the entire duration of the upgrade process. There's no guarantee that leaving the cluster in maintenance mode for the entire upgrade process would always remediate issues arising from skip-version upgrades, in any case.
The docs did not previously note the restriction regarding single-version upgrades. They do now: See http://docs.splunk.com/Documentation/Splunk/6.5.2/Indexer/Upgradeacluster#Site-by-site_upgrade_for_multisite_indexer_clusters -- "If you have a multisite cluster, you can upgrade one site at a time, as long as you are upgrading across no more than one minor version (for example, from 6.4 to 6.5)."
If you need to perform a skip-version upgrade, you have two choices:
You can perform a non-rolling upgrade of the cluster, as described in http://docs.splunk.com/Documentation/Splunk/6.5.2/Indexer/Upgradeacluster#Upgrade_a_6.x_indexer_cluster_to_a_later_version_of_6.x.
You can perform a rolling upgrade in two steps. That is, to go from 6.3 to 6.5, you can upgrade all nodes from 6.3 to 6.4, followed by a second upgrade from 6.4 to 6.5.
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