Like others I too found out that it’s a mistake to sync Safari on the iPhone with Safari on the desktop. While I thought it would be nice to have all my bookmarks on the iPhone what I ended up with was two folders that I just couldn’t delete. “Bookmarks Bar” and “Bookmarks Menu” reside in Safari on the desktop. If you sync bookmarks those two folders end up as seemingly undeleteable folders on the iPhone.

Since restoring my iPhone and starting from scratch is not an option for me, I did a little looking and the only other solutions were for Mac PCs. So I did a little experiment which did in fact delete both folders. Here’s what I did.

1. Quit Safari if you’ve got it running.
2. Goto the Start Menu and search for Bookmarks.plist or navigate to C:\Users\<User Name>\AppData\Roaming\Apple Computer\Safari.
3. Copy Bookmarks.plist to the desktop as a backup.
4. Open Bookmarks.plist from its original location.
5. Highlight everything after “<?xml version=”1.0″ encoding=”UTF-8″?> <!DOCTYPE plist” and delete the highlighted text.
6. Save and Exit Notepad.
7. Connect and sync your iPhone with iTunes.
8. From the Summary pane Unselect the “Automatically sync when this iPhone is connected” option.
9. Goto the Info pane and select “Sync bookmarks with:” option and select Safari. Then select “Replace information on this iPhone” option and select Bookmarks.
10. Sync your iPhone.
11. Open Bookmarks from within Safari on the iPhone. Bookmarks should be completely empty except for the History folder.
12. In iTunes from the Info pane unselect both the “Sync bookmarks with:” and  “Replace information on this iPhone” options. From the Summary pane select “Automatically sync when this iPhone is connected” option.
13. Sync the iPhone.
14. Copy the Bookmarks.plist on the desktop back to its original location to restore all your desktop bookmarks.
15. Your done.

Hope this works for you like it did for me.