Johnny, the way I'd approach this in Pr is to make a separate Sequence in Pr for each of your clips to export. Pr has a subclip function like FCP does, but you can't export Pr subclips as you can with FCP. Nor can you make a subclip from a Sequence the way you can in FCP. So, if you have a reason to put all your clips in a single timeline before you export, what I'd suggest is that you duplicate your master sequence fifty times if you have fifty clips, and then go into each one and delete clip 2-50 for the first sequence, 1, and 3-50 for the second, and so on. Sounds labor intensive, and it would be. If all you're doing is color correction and trimming of individual clips, this may be easier to do in Ae, since you have the suite. In Ae, you can select your 50 clips and drop them onto the New Comp icon, and it will give you the option of making one Comp with all 50 clips, or 50 separate Comps - and I think this might be your best bet, as Pr doesn't give you this option. You can copy effects settings in one clip and paste to another in both Pr and Ae. In Ae, when you send your first Comp to the Render Queue, you can choose your destination, output module (codec, dimensions, etc.), and every Comp you send thereafter will use the same settings. And you can make those settings defaults in Ae as well. Ae also uses multiprocessing very efficiently, and you may achieve some speed gains by using Ae over Pr as well. The exception here may be that if you use CUDA accellerated color correction in Pr (and you have an NVIDIA Quadro 4000 installed), that can give you a speed bump as well. So, this seems to me a case of no overriding advantage to either method. Both will get you there. And maybe a few tests would be in order before you committed to all 50 clips.
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