What Oosh said, you need to have the Dynamic Lighting Layer active, to be able to see and interact with the parts of the map that interacts with player vision when using DL or Advanced Fog of War. Here is a gif that shows how to remove the first door on the map. You make sure you have the DL layer selected, and then right-click on the colored segment that represents the door, which enables you to delete or do other things. You can also move the door to the Map layer so it's shows where the door exists, while not interfering with vision. If you move it to the Map layer instead of deleting it, you can then later move it back to the DL layer if you want the door closed. (You may need to click on the gif for it to play) As you can see in the gif, the module have color-coded dungeon walls with blue, and door/openings with brown. In general, I think most if not all modules have their doors, openings color-coded differently from the rest of the walls to make them easier to spot. For example, Lost Mines of Phandelin uses green for all the walls, and uses red for any doors, hidden paths or other things that might be needed to toggled during gameplay. I'll update the Layers page on the wiki a bit in a few minutes, with points I've brought up here.
