I don't see anything that would unload the loaded file. You should have a line like...
somewhere, such as in code for any buttons that could be clicked to changes sections.
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In case you are using the timeline for the different sections, when you dynamically add content it has nothing holding it to the timeline unless you add it to something that was not dynamically created that lives in the timeline, such as an empty movieclip that you manually place on the stage. If the dynamically added content is not anchored to something then it will persist throughout the timeline.
I am doing the timeline route. So once I have my empty movie clip how do I anchor my SWF to that movie clip?
Where "yourMovieClip" gets replaced with whatever name you assign to the empty movieclip.
PERFECT! That worked. Thank you so much I can't tell you how long I have struggled with this!