Flash has a limit of about 16000 frames that are consecutive. That's true whether it's a single scene or more than one scene. A work around is to have up to 16000 frames in a movieclip in frame 1, and you would play to the end frame of the movieclip, and then step into frame 2, where the next movieclip is. Keep going for as many of those as you need.
If you work that way you can then export it as video from Flash, by telling the exporter to keep exporting for the duration of the whole animation.
Thak you for your answer, would it be possible to take lets say 4 .fla files that are 4 different scenes of one big animation and import them in Adobe Premiere or Adobe After Effects and from there combine them to make one movie clip. It would be like taking 4 short movie clips and combining them in Premiere but instead of being movie clips it would be Flash files. If that was possible I would be able to storyboard my animations in short animation clips.
Yes, that would work. One thing to note, when you do the export to video from Flash Pro, make sure you're using a recent version, and when you export don't check the box that asks if you want to compress the video in Adobe Media Encoder. You want high quality MOV files to take into Premiere. Then you can export media from Premiere at different lower qualities.
Thank you very much, this helps me a lot.