I simply want to replay the levels to achieve the fable entries as I'm missing a few, but don't want to alter the choices I made in the event of a season 2. Does replaying a level alter your choices or have no effect on your save file?
Yes, replaying an episode will alter your choices. Even if you decide to replay the whole episode or a chapter you still have to finish the episode again. Starting a new game is the best way to unlock the other book of fables. You'll want to change your save file before doing that, and don't worry, your progress regarding the book of fables unlocks will remain untouched.
And you can also keep your "canon" playthrough safe that way.
Just go to your first save file, go to the chapter you want to replay, click it, it will ask you if you want to rewind, say yes and then choose the save file you want the rewind to overwrite.
I see, so I can rewind, then save to another file leaving my original intact?
If you want, just choose a blank save file and replay the entire game and just make sure you do what you have to do to get the missing Fables entries in those levels.