If the original disc plays in both 2D and 3D players, you can get that functionality by using the 'clone' option, and it will make an exact duplicate of your 3d movie. (on disc)
That disc should behave in your computer or blu ray player, the same that the original does.
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You can copy a 3D bluray into a 2D movie... I think this is what you are doing and this is the message that you are getting.
And you will end up with a 2D movie.
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Its hard to tell 100% why you are getting this message, your description is kind of vague on what procedure you are using to actually do your backup.
