Ahaha... wow. I just purchased a new multifunction printer yesterday. My old one could do duplex ADF scanning but the new one sadly can't (at least in Linux, I swear reviews said it could scan duplex... or maybe it only copies duplex for some reason). In my spare moments throughout the day I've been piecing together a script to make scanning a duplex document easier.
What operating system are you using? Sounds like you are scanning right to PDF files... what I basically do is scan to TIF into an odd directory and an even directory, then move the first odd file into the parent directory as page-00001.tif, then the last even file as page-00002.tif, and so on. Once they're all in one directory and properly ordered I make a PDF or DJVU file from there.
Edit: Oh, you answered before I could finish writing. Yeah, that's the basic idea - scan one side, flip, scan next side, reorder.