The Kindle annotations actually go by filename, not necessarily the book title. I don't know if Calibre generates a new file with an altered name (I use mobi2mobi and effectivly edit things in place), but usually renaming the .mbp file so that it's got the same filename as the .mobi should keep the annotations.
At least, that's always worked for me with the Baen Free Library books which I've started to read, noticed the author field was wonky, fixed, and put a fresh copy back on the Kindle to continue.
You can also output them to plain text using the
MBP Reader Perl script which someone has very kindly whipped up.