I'm on my 2nd time through and in Part III for kicks decided to go back to Ember (because it was still on my map) I climbed back down into the well, walked all the through the cave and came out in Duskwood. Going to the Map transition allows you to go to the following additional sites (which no longer appear on the map):
Fort Locke
Old Owl Well
Black Lake District
Docks District
Several of the other sites disappear but as soon as you go back to the Keep (or any sites that normally appear on the map in part III) will restore your map to "normal".