Something like this has happened before, in the long long ago...
The source is the renpy stack, where the game attempts a call before it finishes loading and the return data gets messed up. This creates a phantom return point that the game will attempt to return to whenever it finishes loading. I thought I had removed all chances of that from the game as it is obviously not working as intended.
It's kind of the dirty secret renpy doesn't want you to know about. This return point is baked into your save file and theoretically it is repairable. If you want to DM me your save I will see what I can do... but no promises. This is the black magic or renpy here.
Okay, I thought about it for a while and it seems that the issue was something related on my end.
I run a bootleg shadowcopy service on my machine using an externally mounted NAT. This works in a similar way the windows server version does, by making copies of files. These are raw copies and not restoration points and since I have 5TB external storage available, I simply designated my entire 500GB main drive for duplication, meaning I can run a full restoration pretty quickly.
Here's my theory: since that counts as a mounted disk and the stack got copied along with it, it seems Ren'py got confused about it's own state.
Stopped the service, unmounted the disk, ran another clean up, works now.
TIL: Ren'py gets easily confused and it doesn't help what you're doing with the flags here is pushing the limits of the engine. It's pretty amazing though.