During a full site copy where only the structure is being migrated, the SharePoint Designer workflow associations are not being preserved. Most likely, an error message such as the one below is encountered:
Note: The structure copy is one where no items or folders are included in the migration.
When running a structure copy, there are no items or folders migrated. However, it's side effect is that none of the workflow definition files are copied either. These files and folders are stored in the hidden Workflows list and must be migrated when workflow associations are being migrated.
The attached transformer script can be used in these cases. When it finds the Workflows list, it will enable folder and item copying so all the templates are also migrated. Please refer to the Read Me file in the package for additional instructions.
To know more about adding a transformer script within a job configuration, please click here.