Hello, I'm gonna assume you have this issue on the PC version.
Keep your old save somewhere safe, launch the game and start a new game in the same slot you want to replace, go far enough so you can save (right before you enter the twins hatch) and quit the game.
Go to the save folder and replace the save.
It should now work fine.
Sorry about that, I'll investigate as to why this happens and fix it for the next update.