You may want to (or find someone who knows how to) do a surface scan of your hard drive. Pre-SSD hard drives are essentially magnetic tapes miniaturized and in disk form; metal floppy disks. Eventually the tiny magnets that make up the ones and zeroes wear out, and can start to spontaneously lose data. Mine had quite a few sectors go bad, which caused two games to corrupt and the operating system to crash at random long intervals. Hard drives are also built with extra space that can't be used normally due to being too physically small to form a suitable portion of the disk; repair software can tell the drive's controller to remap the dead and dying sectors to this fresh space so that the operating system never knows they moved, but can continue writing and reading properly.
If there are more than a couple dead sectors, it's a signal your hard drive probably isn't going to live much longer and that you should buy a new one to copy it over to and replace it with.