This is why many developers stay on a version thats working for them. Wait until 4.9.1 or later till something like this is fixed since its obviously a bug since you say re-building it from scratch entirely fixes it. Submit it as a bug so that the staff can look at it.
Looking at your project I see no errors after building lighting at preview quality in puzzle3.umap and puzzle3rebuilt.umap works right out of the box so its either a bug, your project, or your hardware. Try verifying the engine and trying, otherwise try reinstalling it and trying.
Don’t forget to accept an answer that best clears your question up or answers it so when the community finds your question in the future via search/google they know exactly what you did to fix it/get it going as well as keeping AnswerHub clean so that it gets removed from the “unanswered questions” category.