The fact that Panorama modifies library files when it shouldn't has been a long running issue. In the past, this only caused a problem when running under certain permission configurations, for example if running under a different account than the one it was installed under.
The new alert appearing is almost certainly because in the past, Panorama wasn't calling the canCloseDocumentWithDelegate method correctly. When the project was converted to Xcode 8, the newer version of Xcode flagged the problem so I fixed it. So the problem was really there all along but masked.
Figuring out how to 100% prevent a Panorama library database from ever being modified has been on my radar for a long time, and it is tricky. Last night I made a new build that tries some of the ideas I had listed in the bug issue below, but unfortunately they still didn't prevent the files from being modified, so back to the drawing board.