Hey,
you can swap Tiles on your Map with the following call script:
$game_map.data[x, y, layer] = ID
x = map_x position
y = map_y position
layer = Map Layer, it starts with 0 for Layer 1
ID = Tile ID from your Tileset, starting with 384 for the first Tile below Autitiles in the left upper Corner
Though, i don't know if the changes on the Map are saved in the save File. I can't test it yet because i'm not at home. If not, maybe some friendly Scripter could edit it so the changes are saved.
greetz