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As I am strictly a Linux user, I'm not super sure of where Godot (the game engine) saves user data for Windows.
Here's from their documentation:

Windows: %APPDATA%\Godot\app_userdata\[project_name]
macOS: ~/Library/Application Support/Godot/app_userdata/[project_name]
Linux: ~/.local/share/godot/app_userdata/[project_name]

I have no idea what "%APPDATA%" means though... But maybe you can search for the folder "app_userdata" and find it. I should probably update the patch notes with this info.

As for the window positioning and size, I have no idea. Looked a bit at the code but don't think I do anything special with the window.
My one idea is that maybe the default size of the window (1536 x 864) is bigger than your screen resolution (if for example you use 720p), and that makes it flip out?

Thanks for getting back to me! I'll poke around, see what I can get to work.

Looks like it's (whatever your drive is called)/Users/(whichever account the game is installed on)/AppData/Roaming/Godot/app_userdata/Xess

AppData is hidden by default, and while I'd known to check it, I was having trouble finding Godot. Search function found it, though. Thanks!