I have been experimenting with python and the sqlite3, ctypes, struct, pyPdf and reportlab packages to create a PC based tool to merge annotations with pdfs. I now have an experimental version that I tried with a few files and it seems to work. Still a lot of work is needed to get it 'user-friendly'.
For those that have some python experience I attached the code. At the top you find a directory variable it should contain the (relative-)path to a directory with books and a metadata.db file (copied from your DR).
Please let me know if it works (or what goes wrong).
I am using python2.7, the extra packages that you need can easily be found with google.