I think anything can work if it's done really well. I can't think of any books that do what you're talking about off the top of my head -- maybe someone else can?
With this idea, it would be important to make sure the story still has a strong arc and a satisfying conclusion. I'm imagining a story in which the characters don't learn what's in the box or whatever, but they learn or achieve something else that is more important, so the original mystery is almost forgotten by end.
If you have an idea and think it would work, there's no reason not to write it and see how it goes!