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I had this issue back in Godot 3.5 and hoped that it'd be gone, but Panels and some other Control Nodes still resize magically when executing another scene. This is such weird behaviour, that I have no idea where it might come from. Has anyone ever seen such a thing happen before? Here is a video of the bug in acton: https://piped.kavin.rocks/watch?v=79DYDT5qngk
This is just a guess but it could be that (re)setting the texture of an control node May also reset it's size since I think it tries to stick as close as possible on the original texture resolution.
Is the size a different when you set it to a different texture? Maybe the same image but with lower res?
Clever thought, but no, the code doesn't change any of those textures, it just changes the character portrait and the background image, which both don't mess up anything. They are still where they are supposed to be. Thank you either way!