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If you don't have linux you can always split files with pdftk. Just cut the double sided into two files, odd.pdf and even.pdf then run:
pdftk even.pdf burst output %04d_A.pdf
pdftk odd.pdf burst output %04d_B.pdf
pdftk *_?.pdf cat output combined.pdf
It'll take your odd and even pages and put them in the right order.
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