There have never been best practice within this migration except to invalidate all old users by disabling all of them and creating the new ones. This will make everything consistent, even the record entered with the old USERID (that will have a orphaned SID, of course).
In your case, having completed the migration, you only have to use batch jobs to amend all of the orphaned USERIDs in related table if you want to clean them up. If they do not harm, you could even leave them there.
Rest assured that NAV 2013 R2 is out of mainstream support and it would be strongly advice to upgrade to the latest and greatest version.
You might take the chance, instead of a cleaning up now the database, to create a new implementation project instead of an upgrade and only move master data and open entries into the brand implementation (instead of upgrading)
