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I don't know what editing you require but if it's simple cutting/looping then you can probably do it losslessly in some thing like eac3to/delaycut, this will keep the original encode intact along with the EX flag (I think)
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The rear center info is matrixed into the original mix. You can't get rid of it unless you're remixing from the ground up. Most tracks aren't flagged anyways. Many films on bluray do not have these tracks listed or flagged and are just plain 5.1 but if you listen for it or decode it out the info is still there.
Damn Fool Idealistic Crusader