What I'm not clear on here is how this affects the source control integration.  Let me explain the scenario:

• MyApp has been developed in Dev and linked to Source Control.  It is in the Custom Application [sys_app] table in Dev.
• MyApp 1.0 has been updated in Source Control and published to Prod via the Application Repository.  It is stored in the Store Application [sys_store_app] table.
• Prod is then cloned down to Dev, so Dev has the Store App record.  Not only have we lost any updates we did since 1.0, but we have also lost the Source Control link, right?  So after we convert back to Development mode, is there a way to maintain the link to Source Control that we had before we cloned?  I'm guessing that the Repository Config should still be valid since the app record is still the same, it has has been reclassified.  Testing this theory now, but I have heard anecdotally that it doesn't work and that you cannot relink an existing app to the same source control.  Anyone experienced issues with this?