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The approach to update application is correct. After you select the package, it is expanded to the system 8n the form of the original form. Once in monitoring mode you can edit or copy over that file. When you want to save the package you have a choice to save the package as an update or as a new package (with new pkg name and id guid). If this is a file that will naturally be openned for write (whether or not it actually changes) AND the package has been deployed, you probably need to use the save as new package option, remove the old app and supercede with the new.