Lots and lots of very precise data logging on almost every single channel at multiple points of the vehicle with accurate and synced timing. This makes it possible to trace which signals start getting lost at what time and position relative to one another. This would probably get them close to where they need to be. Then it becomes a deep dive into all data logged during production (measurement reports, photos, etc) to find anything that stands out and formulate theories on what might have failed for what reason. Put all of that together and they can quite accurately tell what is the most likely thing that happened, possibly performing some extra testing to prove or disprove the theories. Sometimes it remains guesswork though.