So out of the 6 maps he starts with, he only actually sells 3 of them. The Hamsah Map, the Western Thera map and one of the Eastern Thera maps are not typically for sale here. So when you bought those three maps, that is why they were not replaced in the shopkeeper inventory.

When you attempted to buy the second Eastern Thera map, it was replenished because that version of the map is sold by the shopkeeper.

There are two different versions of the map of Eastern Thera that are identical at face value but still different objects which is why the shopkeeper had and sold both versions.