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This script is similar to my original script for interleaving two PDF files (see: http://try67.blogspot.com/2008/12/acrobat-combine-even-odd-pages.html), but it works as a batch process and can combine entire folders at the same time.
Basically, you select the folder that contains the odd pages (1, 3, 5, etc.) and the one containing the even pages (2, 4, 6, etc.) and then the output folder, and the script will interleave all files with the same name in both folder and will save the combined file in the output folder.
If you have any questions regarding this tool, you can contact me directly.