I’m having similar issues and is why I have ended up on this thread. My top navigation bar and categories have disappeared. Everything was working properly until I changed the callouts and footer .phtml files (which I have now replaced with original copies). I have ensured all the categories are still in place, active and anchors. I have checked the store management the root category is set appropriately, I have refreshed the cache and indexes, and still my navigation top bar is missing. I have tried rewinding my server a few days and still the problem exists. I’m completely stumped. Any advice would be greatly appreciated.
Also, my left and right callouts and site map from my footer have also vanished.