The disadvantage of splitting the thread is that people on a higher level won't come to threads of lower mission to help others. When someone got stuck in the mission he/ she has to hope that someone on the same mission knows the answer.
A better system in my opinion would be, to make a general rule, to write in every post in which mission the person is, like a heading. So it would be easy to get the infos needed by using the search function and then search for "mission 1" for example.