Pressing "Start Game" shouldn't reset the persistent data. It WILL change the title screen -- the title screen is set up so that it will return to the screen for whichever the last save filed you played. So if you start a new game, it will go back to the default screen, if you load a save game in arc 3 and play for a while, it will change to the arc 3 title screen, etc. However, it doesn't delete anything in the CG or replay galleries or anything, so that is what is a bit concerning.
I'm really at a loss as to what it could be... 😭 I've never had anyone report this strange error before... I can try to hunt and peck around Google to see if I can find anyone else ever having this error with Ren'Py games but I'm not sure if I'll be able to find anything 🤔