You can't move application-icons manually without breaking ApMeFo's folders. You'll have to move the Phone to the folder via ApMeFo, since otherwise Hildon comes in and restores the menu to it's regular state. So in short : don't move icons from menu without ApMeFo, you'll just break the folder, since ApMeFo is not a plug-in to Hildon, it's a separate program to modify it.