Guide on Deleting a Village
There have been many people asking how to completely delete a village or the wand of negation not working properly. Here is what I have done to completely remove villagers and buildings if needed.
1. Kill all villagers and use wand of negation.
2. Now you need to find the coordinates for the center of the village. Go into the town hall, fort, etc and press F3 and note the X coordinate.
3. Close out minecraft and browse to AppData\Roaming\.minecraft\saves\XXXX\millenaire\buildings, where XXXX is the world you want to remove village from.
4.You will find in this folder a bunch of files that begin with numbers, these files represent properties for each village based on the coordinates.
5. Refer back to X position of the village and find all the files that begin with the X position. EX: If the center of the town hall had a X position of -10, the files would start with a number around that. It could be -8,-9,-7,-12,-11, ect. Now delete all the files associated with that village.
6.Now go back one folder to AppData\Roaming\.minecraft\saves\XXXX\millenaire and open up the villages.txt or lonebuildings.txt, depending on what you destroyed, and find the village/building that matched the coordinates in the buildings folder and delete that from the txt file.
Now, if you restart minecraft and go back into your world, the villagers of the destroyed village/building will not return. I have created several villages and have done the above to each and works every time.