Hacks My Clippings: Linking new versions of books to previously clipped content

[fatso]

I manually make pdf->txt->html->mobi versions of long articles I get on pdf to make them readable on my Kindle. Usually I find some errors/omissions in my conversion (missing header, links, etc), and I rebuild the document.

Unfortunately this makes all the notes (made for the previous version) disappear when opening the new version. Even if title and authors match this happens. This is really not a big mystery - the Kindle probably does a hash of some sort (md5?) of the book, and if that does not match, then it makes a new entry for the book. And so the previous highlights no longer apply.

BUT what can I do to manually edit the MBP1 or MBS files to re-establish the connection between my notes and the new version of the article?

Since the textual content of title and author in "My Clippings.txt" is identical for the new version and the old, I guess the actually used data must be in either My Clippings.mbp1 or My Clippings.mbs. With so much hacking going on, I guess there must be some kind of tool for this? If not, I am a developer, so I can compile my own sources, if must be