I recently tried out the Fetch Annotations feature following the instructions provided in this forum at http://www.mobileread.com/forums/showpost.php?p=817749
When I got to the very last step (#9) to Confirm the Changes, I noticed that my Notes and Marks were now blank. However when I connected my Kindle Fire back to my PC, I discovered that the updated MPB file, which you transfer back in step 7, actually gets saved to a subdirectory of the author's name beneath the documents directory, instead of in the documents directory itself where the actual book is stored. I moved that mpb file back to documents, deleted the subdirectory, and all my marks were back. Yay!
Will have to wait and see how it all works out trying to sync my notes & marks this way from my Kindle Fire to my Kindle 2 but at least I found that my existing marks weren't deleted after all, which looked to be the case at first.
Just thought I'd mention this in case it helps anyone here.