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Since the nav is being created for the first time, its complete ordering is taken from the existing NCX while may or may not follow the OPF spine order as that was not a requirement under epub2 although it tends to follow naturally from the playorder attributes typically used in the NCX.
So before running ePub3-itizer you may want to verify that the NCX playorder matches the spine order to be safest.
Hope this helps.
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