Manipulating Google Chrome bookmarks from external program (and make Chrome aware)?
%LOCALAPPDATA%\Google\Chrome\User Data\Default\Bookmarks file is protected by a checksum for writing errors. Google Chrome make a backup of this file as Bookmarks.bak. So if Bookmarks file is corrupt, Google Chome uses backup file for restoring bookmarks.
Checksum operation is a bit tricky. You can look at it's source (as Chromium project is open source). It seems that Chrome does MD5 calculation on every bookmark's:
idtitlefolderurl
So you can look this source code for investigate further.
But i do not recommend to do this. Google may change this format without any notice and your software suffers incompatibility problems. It would be better to write an Google Chrome extension and interoperate with your desktop software.