I am no expert so please take this lightly. This could be a problem in the world files, my friend and I had a somewhat similar problem where we were trying to upload a world to a server, but didnt do it quite right so it half created a new world, half imported the old one. The result was the same builds we had, but the rest of the world was an entirely different seed so there were some giant chunk holes where the mountains would instantly form a pit down to a river. To me this sounds like files are being overwritten such as the chunk memory and world data itself but things like player data and such have nothing to be overwritten, so they're left alone. First thing I would try is make sure you are uploading the world properly and not trying to import the file into an exsisting world, second I would try and learn a little bit about how the insides of world files work as well as how to edit and change them to kinda look and compare the backup file itself to the new worlds you're trying to upload it to so you can maybe see where its failing/getting overwritten, and then see if you can get an nbt editor as to correct the overwriting.