I'll be honest - I'm not sure why the waterfalls "moved" over, but for the meshes, did you save all of those objects into new object groups in object maker? If not, you'll basically have to add those meshes again while their in their own groups.
This usually happens when you save them in an old object group, including the default groups. Try saving them all in a new object group. You can delete the old objects after placing the new ones in the map with the old ones.
I hope that helps with the dissappearing objects.