my world has been merged with a past version of itself

i have been playing this survival world for a couple weeks and nothing has  gone wrong with it until now and i have no idea how it has happened but my world has merged with and older version of itself. so basically stuff i did in the past and destroyed and rebuilt over it has come back but it has merged with what i already had there. its like i have built a chest room in my house but half of it has been covered back over from before i built it, also i built a armory room and had armor stands but when i went back in the armory room it was all covered back up from before i built it but i mined my way to where the armor stands were and it was covered with normal stone. i have no idea how this has happened or why its happened. it has also removed some of my chests which had some of the most important things i needed to finish the game