You would duplicate the app in the QMC\Apps area and then delete the published copy.
Then the app will be in your 'my work' location unpublished. Its in your 'my work' as long as the QMC lists you as the owner of the app. Again this is in the QMC\Apps location.
Seems a little strange but that is the method.
Keep in mind that any user/personal content (sheets, bookmarks, stories) that users have created while the app is published will be lost.