With how glitchy Houses, stronghold and TC are placed, you need to introduce a new building system.
Make a new deeds for all buildings, fix the placing issues and the fact that you can grieef town with houses.
The new deeds will take over the build in the game and you should give players a 3-6 month warning that the old legacy buildings will decay after that period.
This will wipe the current buildings of the map, that has been placed in legacy time, building with trees or mining notes inside etc.
Make a new deeds for all buildings, fix the placing issues and the fact that you can grieef town with houses.
The new deeds will take over the build in the game and you should give players a 3-6 month warning that the old legacy buildings will decay after that period.
This will wipe the current buildings of the map, that has been placed in legacy time, building with trees or mining notes inside etc.