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I believe that using optical flow makes Motion render the entire source file... I would create a new master clip of just the footage that you'll use and apply optical flow to that.
 
That's what I did. To render the source Motion wanted over 8 hours! Promptly canceled that and sent an individual clip, 9 frames long. Extended it to 60 frames using optical flow and once it was done attempted a RAM preview, which prompted a very nerve racking Finder warning explaining that my system disk had run out and that I needed to shut down some apps. :eek:
 
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