If you have recently run a scan with Privacy Controls, it is possible your Chrome bookmarks were removed.
 

This is because Chrome stores bookmark data in a single location that is also used to store information about your browsing history. When your browsing history is removed, you may also lose bookmark information.
 

To prevent Privacy Controls from removing this information in future:
 

  1. Please open Privacy Controls and go to Options along the left hand side.
  2. Select the More Info button along the right hand side, next to the internet browsing history section.
  3. Expand the category that corresponds to Chrome clicking the + (plus sign) beside "Google Chrome".
  4. Now deselect Browsing History, along with any other categories you do not wish to have cleaned.
     

To delete any browsing history from Chrome manually, please use the instructions here.