Nested movie clip disappears

I am working a very complicated "lesson" in flash. I am by no means a flash expert, but I have deduced that a movie clip "disappears", not every time, but frequently. Can a movie lose its reference? I have been doing some research and i have read that instantiating clips with new can make flash lose reference. While i do not think that was there approach, i have noticed that they use the assignment operator for clips, would this be the problem. If not could somebody give me an idea of what would make the movie lose reference on occasion? I know i should bring up the code, but the code is spread over 150 pages, but if necessary i may be able to do something.