It's done with a panorama script I wrote and blank maps.
First, I took screenshots of the maps with monochrome tilesets, then the same maps with only the color orange in the tilesets. Then I pasted the screenshots together into images. Then I made a series of panoramas, I think they ended up being a couple hundred images, with the colored screens covering progressively more area. I used a Photoshop macro for that to take most of the gruntwork out of it.
Then I used an event to show each panorama in order on the blank maps. That way, I could still have the characters above the panorama looking around and moving.
First, I took screenshots of the maps with monochrome tilesets, then the same maps with only the color orange in the tilesets. Then I pasted the screenshots together into images. Then I made a series of panoramas, I think they ended up being a couple hundred images, with the colored screens covering progressively more area. I used a Photoshop macro for that to take most of the gruntwork out of it.
Then I used an event to show each panorama in order on the blank maps. That way, I could still have the characters above the panorama looking around and moving.