Actually it's worse than that...
Every version of the Atlases is different from the other. There's things that can only be found in Atlas 1, other things can only be found in the Atlas 2, and others can only be found in Atlas 3... and then there's the things that can only be found in Emer's Atlas Addendum.
The things missing from Atlas 1 in Atlas 2 are minimal ( I remember that a few NPC went away from the Navigators and Loremasters for example ).
In my case if I had to worry about duplicate... *look at the MERP books, with the reprints, the cover changes, the 2 Mirkwoods in a book*
I think I have 4 versions of Northern Mirkwood all considered. ( and yes I have all the Master Atlases
)