Replace a Clip with an Image Sequence CS4

I edited a lot of footage in PP CS4 that had a green screen behind it.  i used proxy .mov files with the plan to replace them later.

I have created an Image Sequence via After Effects, which I imported to PP.

Now need to replace the .mov I used as a proxy.

The snag I am facing: I can't figure out how to replace it.

I've scowered the web for an answer.

If I replace it in the time line, it replaces every edited part with the image sequence starting from 0:00

So it kills all those edit points.

If there is no way to do it, does anyone have any advice how to export from After Effects so the transparency is still there, and I would be able to replace a proxy .mov in PP?

Thanks!!