Thanks for the info.
So, from what I understand, there is a separate branch of fate saved for any file that passes reaches 6, and the game just loads from the most recently used file. So if I did a lunatic run past chapter 6 and then wanted my hard branch of fate back, I could just reload my hard mode save and then branch of fate from there.
This is a lot better than my original worry, that there was only one branch saved in the game and that if I saved a new file on chapter 6 that I would lose my previous "RNG blessed" branch.