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I am upgrading 2013 to 2016, copied Secured store DB and Created Secured store connecting it to the DB with passphrase, but after all done the target applications, are missing, any help would be appreciated.

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The first problem was the Update-SPSecureStoreApplicationServerKey : Master secret key is not present in the database. I used script to change the key from link: SharePoint 2016 - Secure Store - MasterKey cannot be set! Problem Solved. That worked , except no target Applications got transferred. Deleting App with data, re-importing DB and recreating SS App with PS from https://docs.microsoft.com/en-us/sharepoint/upgrade-and-update/upgrade-service-applications-to-sharepoint-server-2016 Solved the peroblem.

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