make the cut segment be a new video.
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Well, you can, but you can't output it as mpeg. You can use an mpeg2 editor, as suggested above, or output to a different format, or frameserve the segment to an encoder. Only an mpeg2 editor can preserve the original quality without re-encoding the lot.
Read my blog here.
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Checkout Cuttermaran (freeware) in conjuction with PVAStrumento (freeware).
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