I’m away from my PC for a while. I know the unfold and flatten plugin that works with 2017 can be a little wonky.
Try orienting faces before unfolding and flattening.
Do as few pieces at a time as possible. Like the side of a fuselage, then the top, and then bottom. Save a flatten by copying and flipping the side to make the opposite side. Layout the pieces together again.
Only flatten outer surfaces, not the fully thickened piece.
When I get back to my PC, I can give more specifics.