Well, one can look to our society: we have a habit of building cathedrals, churches and other religion-based buildings over existing ones. Basically, the old becomes the foundation for the new. In the case of Gobekli Tepe, the older sites (at the bottom of the hill) are backfilled so that the newer sites can be constructed right on top of the existing enclosures. They were no doubt making slight changes to their religion over the years, so the need for new places of worship was needed. Perhaps these changes are not something obvious to us, but to them it must have been a huge difference.