Event #2 creates all the Sprites in a rectangle and event #3 removes the sprites not overlapping. So to actually make it delete tiles you need a new event below all that:
Mouse button is down
for each tile
--- tilemap: erase tile at (self.positionToTileX(tile.x), self.positionToTileY(tile.y))
To make it only happen when you need it, put all the events in a group and disable/enable it as needed.