Don't save the data in the characters then, you can store relationship info the same way you currently store stats and gold.
Any particular reason you have things set up that way? I haven't messed with Renpy to much but from what I know usually you just have a flags list/file that stores everything rather than splitting data between multiple things. I've been messing with doing a VN-like game in Godot and thats how I've been handling it there.