You can create custom validation logic to determine if a download file should be applied to a remote database. You do this with the sp_hook_dbmlsync_validate_download_file stored procedure. With this stored procedure, you can both reject a download file and override the default checking of the generation number.
You can use the dbmlsync -be option to embed a string in the file. You use the -be option against the file-definition database when you create the download file This string is passed to the sp_hook_dbmlsync_validate_download_file through the #hook_dict table, and can be used in your validation logic.
For more information, see sp_hook_dbmlsync_validate_download_file.