Ok, this is weird but it seems to work. If I have two duplicate places, I choose the second place on the list**, then copy that name (although it is identical to the other one) and paste it onto the duplicate name above. Doing it the other way around does not seem to work.
There is one more thing, the name will auto fill, watch whether you pick the first suggestion or the second, that way if you try it twice you do not pick the same one.
I have checked and so far it does not seem to remove any places from the facts page.
** or pick the duplicate name with the most people in it as your source for copying.