copying to another song will mean some tracks in one song and other tracks in another song. Since this would be useless to anybody trying to play along with a specific song, it should be pretty obvious that all tracks need to be in the same song besides there was no mention anywhere of changing songs.
If Tr9 is still assigned to Part5, it just means you have not followed the instructions properly to copy RT1 into the correct track - perhaps not even into the correct song!