Attached is a little python program I cobbled together to do merging on the Mac. Don't have a device to test with at the moment, but it seems to work with the examples posted earlier in this thread. Just run and hit file->merge pdf, then select a PDF. The metadata.db needs to be in the same dir as the PDF. It should generate a <input filename>_merged.pdf
It's very rough around the edges, and will quite likely only work on 10.5 (it may also just fail to work for unexplained reasons

). The source is available in the .app if anyone's interested.
If a merge doesn't work right, I can try look into it if I have the pdf and db.
Cheers,
Ross