Apple Animation 1280x720 to ProRes codec??

A friend of mine is receiving Quicktime files that have been doctored in After Effects (PC). What I see is an Apple Animation Quicktime 1280x720 ... where everything but the subject matter has been blacked out: nicely matted so the black becomes transparent. It's obviously an alternative to Green or Bluescreen. Her computer can't handle the file size of that particular codec. It just chokes on playback the moment other tracks are added.
I'm wondering if there is a way to convert the animation file to something in ProRes and still maintain the alpha channel or whatever it is that he has created to do the matte. I tried to do a conversion from the Apple Animation to ProRes SD 16:9 (something the computer could handle), but whatever is causing the matte was flattened, so the black no longer has any transparency ... and no setting in the composite modes does the trick.
I'm in unfamiliar territory. I can't reach the fellow doing the matting - I talked to him briefly a week ago to find out he is on a PC After Effects and can't do ProRes or some other of the more familiar Apple/FCP formats.
Could anyone suggest something? A way to convert to a smaller footprint format, and maintain whatever it is in the Apple Animation file that's creating the black transparency?
All ears,
Ben

Hi -
I am not sure what the problems is - unless she is using a very high horsepower computer with a lightning fast RAID, she is going to have to render when she drops the Animation to the timeline - therefore I would just edit the animation to the timeline, make whatever scale and position changes she needs to make to get it to fit above her background video properly, and let it render. The rendering will composite the animation on the background in the codec and frame size of her sequence, and she should get real time playback as soon as the render is done.
Unless, I misunderstood the question . . .
MtD

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