Perhaps using only one save file with all of the achievement switches and the main game's progress on that file will be less complicated than having the game's progress in one and the achievements in the other.

The only thing with that is using that method, achievements are tied to the player's data, and if they completed the game once, then they could get numerous instances of these achievements if they start subsequent playthroughs. So I'm planning to add a new "IsCleared" switch, which by default is off, but once you complete the game once, it will be "on" and when it is "on", then you will be teleported to the same character selection screen but once you select your character, it will not reward the player with achievements during that playthrough (since they have unlocked them already).

Also along with that, in order to manage each character's storyline and whether the player has cleared the game with that character, then separate switches will be created for these characters. By checking these switches are on or off, then the story will progress as according to these characters' scenario and if the player has cleared the game once, then each character choice in the character selection screen will be marked as "Cleared".