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Here is how I would probably do it:
1. Split the PDF into multiple PDFs such that each PDF has either all one column or all two column pages.
2. Run these files through pdflrf and put each LRF in a separate folder.
3. Use lrf2lrs on each of the LRFs to extract the PNG files (this is how pdflrf has stored the content in the LRF).
4. For each folder, merge the PNGs back into a PDF (keeping the correct page order).
5. Merge each of these newly created PDFs into a single PDF.
6. Run this PDF through pdflrf to get the final LRF.
I think this would probably work but there might be some image quality loss along the way. Hopefully someone has a more elegant solution.
Any chance you could PM me the PDF so I know what I'm dealing with?
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