When exporting as video, you have to keep in mind that all actionscript will be ignored. You can't even use MovieClips for nested animations - they won't play. You have to use Graphic symbols for nested animations. The video output is exactly the same as when you scrub the timeline in authoring environment of Flash professional.
So you might be required to do some editing before you export it as video.
Option without editing flash document would be screen capture using some free screen capture tool like camstudio.