i had problems with things before, if its just a generic building and you have no problems building it again, try deleting the building and build it again from scratch
but
if you have the problem which i had before with certain things which makes the things reappear on the original position after deletion and reloading, then try moving said building out of the map into an area which is definitely not accessible by players, that way you are sure it wont respawn on the original spot as invisible gamebreaking something and you can start working on your mod again
