I had made an underground bunker and began expanding it to include an underground garden and I fully excavated and cleared the cave and finished my structure, only to come back later to find it all filled with stone and only certain pieces of progress I had made were saved, like a glow stone chandelier or a small wood building. A chest underground in the same area has became invisible and unusable, the world also becomes like an X-ray and I can everything around me at certain times.