You might check out this third-party plug-in for InDesign. It may or may not help you (I've never used it). I just saw it on the new Adobe Exchange (beta in Adobe Labs). Here's the description:
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Output Factory automates printing and exporting from Adobe InDesign. Export as single pages with variable file names, output layer versions, update modified links on the fly, preflight InDesign files before output, output to several format at once and much more.
Just select the documents, adjust settings and Output Factory will do the rest for you. Keep working with other programs while Output Factory processes InDesign files in the background. Or leave it working overnight to output hundreds of documents, and the job will be done when you return in the morning.
• Output multiple InDesign files automatically
• Output as single pages
• Automate printing and exporting to PDF, PostScript, EPS, Flash, IDML, EPUB and several image formats
• Output files to multiple formats at once
• Layer versioning: output layer combinations as single files
• Update modified links automatically
• Variable output file names
• Preflight InDesign files and final PDFs
• Supports books and booklet printing
• Send output files over Internet and locally
• Detailed output history
- Adobe InDesign CS3-CS6
- Mac OS X 10.5 and later, Intel-based Mac
This is in the NEW Adobe Exchange in Adobe Labs. You can read about it in a post I just saw on InDesignSecrets.com:
It's from Zevrix Solutions so you could probably get info on their website.