Yes, it appears that document is out of date. Thanks for pointing this out. The NiFi Admin Guide  has current information on how to manage access controls via the new files.
The state directory stores valuable data for cluster coordination and other features but is not related to user access control.
Do you have a specific question with regards to performing your upgrade? Hopefully we can help.
If you can, please open a Jira to update this documentation.
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Are there updated NiFi docs for upgrading NiFi's that have the new access controls? eg. 1.3 -> 1.4 or 1.4 -> 1.6? There looks like a couple more files that need to be moved over... users.xml, authorizations.xml.. I copied over the state folder (although I'm not sure if I had to)