If you still want to receive an item when destroying a village, you need to switch around the Layers of the Tile changes.
This is for the normal tile changes are layered:
but if you want it the way you described above:
look that the Destroyd Village Layer is above the respective Saved village layer.
The ID for your Destroyd Village should be lower than the ID for the respective gate.
e.g Village1Close has ID 2 while Village1Destroyd has ID 1
You can manually trigger the map changes and make them different depending on which phase it is.
See Arch's tutorial on map changes, turn events and event ID's.
/// This is an a little longer chapter
http://feuniverse.us...struction/110/3/// Location Events and other (IMPORTANT)
/// These are 3 Short Chapters
http://feuniverse.us...struction/110/8/// Tile Changes (IMPORTANT
http://feuniverse.us...struction/110/9/// Event ID handling
http://feuniverse.us...truction/110/10/// Event ID handling