I thought about making a pinball game with godot as well. Glad to see its possible.
I think the ball is respawning for a frame before it disappears again.
I looked at the code. I think you can't reset the ball in a single frame, but maybe set it to static in one frame and switch to rigid in the next frame.
I hope you continue working on this game.
About the pck-File. You can enable in the export settings that it will be included in the executable.