If your custom data was not retained in the upgrade, you must manually copy the data from the version 3.5 or 4.0.1 backup files (deploy_backup) to the upgraded directories.
You must also copy any data you want to retain if you have made any custom add-ons or modifications to the Application Engine installation being upgraded and chose not to keep these changes after the upgrade. You should manually copy any other custom data you want to retain to the upgraded files listed in "Preparing for Application Engine upgrade."
When you have completed the manual copy of your custom data, deploy the Workplace application.