I want to collapse a complex scene with all different layers and different transparency into a single layer (or as few as possible) to optimize the flash file for online (were experince proformance issues).
I have tried the combine and manually copying pasting into one layer but it cuts the fill below and replace with transparent fill. I want to have a end file that is 100% solid.
Is this possible?
You can create groups and then paste all your groups in a single layer. That won't 'cut' them into each other and the transparency should be maintained. It won't help you with performance though, since the complexity remains the same.
If you have tons of complex vector shapes, it might be a good idea to create a transparent PNG bitmap from illustrator.
That may increase your filesize but it will give you a tremendous performance boost.