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Something may be wrong then. If you have an HDV sequence, and your movie from After Effects is HDV of the same resolution and frame rate, you shouldn't need to render. On the other hand if the movie is animation or apple pro res it would need to render.
The best thing to do I think, is finish editing your project in FCP, then before your final export change your sequence render settings to apple pro res, you'll have to re-render but the quality will be better than rendering HDV. At this point it would be good if your clip from AE was apple pro res, but it may be a pain since you'll need to render during the editing process.
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