The doubt is supposed to stay with you! You need to make sure there aren't other causes or contributing factors hiding behind 'the obvious'. There have been notorious cases in spaceflight where the issue was 'identified' and 'fixed', only for the same thing issue to happen in the next mission.

Nothing of the level of rocket failure, but I've tracked down issues where you are never sure of the cause. You keep the doubt and let it drive you. You aren't as much sure of a theory, as you have the theory you most want to disprove and keep failing to do so. The more you fail to disprove a given theory while other people with their own personal 'targets' do end up disproving them, the more you can report that the theory is the reasonable conclusion. But you never given up the idea of looking to disprove it. Eventually others join you and work to disprove your theory. As the group continues to fail to disprove it, it becomes the officially stated cause unless someone can provide evidence otherwise.

Sometimes I'll have one that I'm stuck on for a month before finally disproving it, and it is an interesting feeling. There is some level of happiness I succeeded at my goal, but it is very bittersweet because it normally was my last working theory and now I'm simply lost until I can formulate a new one. Sometimes disappointment in myself that I might've missed some easy way to disprove it for so long, but other times the way to disprove it was sufficiently hard enough that I just accept it is what it is.