Comment 2 for bug 62304

save the original entry/entries from the desktop file together with the changed file. Maybe in the case of an error, check the saved entry with the one from the desktop file to see, if they changed. In my use case, the Exec entry saved by alacarte and the original entry (not yet saved) by alacarte are not changed and you can safely update from the desktop file. In other cases, the user could be asked.