Setup: After syncing bookmarks from the computer to the iPhone
Where: Safari bookmarks folder on the iphone
Problem: Can't delete the "bookmarks bar" and "bookmarks menu" folders
EDIT with solution:
https://forums.macrumors.com/threads/526262/
1. Close Safari
2. Move ~/Library/Safari/Bookmarks.plist to the trash
3. In iTunes, tick the option to sync Safaris books on the Info tab
4. Verify that the folders have disappeared from the iPhone/iPod
5. Clear the checkbox so you never sync Safari bookmarks again (these folder will return if you do)
6. restore bookmarks.plist from the trash