Not quite sure what your question is but as far as I understand that you would like to know how Data or entries in Database get orphaned becoming irrelevant to the application.
1. I am not sure about your example but an entity with an Auto Number attribute or attribute of any type for that matter doesn't get committed to DB on creation or change or on not clicking Save without you explicitly adding the commit activity somewhere on the flow.
2. It's not for the Modeler to manage the data you feed in the DB it's the devs responsibility. One should be aware of things like association handling (Deleting/Retaining the assc. object on delete of the parent or child), to define an entity to be persistable or non-persistable. It's things like these that will save you from heart ache when it comes to DB management.
Hope this sheds some light on your query?! :)