iApp source template has changed post 12.1 upgrade impacting traffic

I recently tried to upgrade one of our LTMs from 11.5.3 to 12.1.0 and noticed that all of the iApps were showing the 'Source Template Has Changed' warning. After the upgrade users reported that the iApps were not passing traffic. After troubleshooting we discovered that re-configuring without making any changes fixed the issue. There are over 4000 iApps on this LTM so re-configuring manually through the GUI is not a good solution and I opened up a case and was provided a CLI command. They didn't indicate that this was a know issue and I have seen some questions on DevCentral about this topic but nothing stating that the warning is impacting traffic. From what I have been told, the template warning shouldn't impact the traffic because the original template should still be used by the iApp and function exactly like it was prior to the upgrade. If this is true, is there anything else that could get change when re-configuring the iApp without making any modifications?