So, ich habe eine Lösung gefunden ohne das man das iPhone neu aufsetzten muss.
Es hat funktioniert!
Falls es jemand anderer auch noch braucht, hier die Anleitung wie es geht:
1a) Quit Safari on your computer.
1b) with you iPhone sync'd to iTunes, unselect the sync automatically box. (You can go back later, just do it for now.)
2) Navigate to ~/Library/Safari/Booksmarks.plist file.
3) Make a copy and rename it Bookmarks(original).plist. This is your backup file in case things go wrong.
4) Launch Safari.
5) Create a new folder called Bookmarks, or whatever you want your top level Bookmarks folder to be on your iPhone.
6) Drag all folders and urls that you want for you iPhone into this folder.
7) Arrange it the way that you want. You can also do this on the iPhone, but it is easier to do it here, than on the phone.
8) QUIT SAFARI AND DO NOT RELAUNCH IT. (This is important, because you are going to edit this file to remove those folders and Safari will recreate them if you launch it.)
9) Open your Bookmarks.plist file in the Property List Editor.
10) Navigate to the Children arrow and expand.
11) Select the "0" item and delete (That is the Bookmarks bar, or Bookmarksbar menu that Safari hard codes to the bookmarks list)
12) Select the "1" item and also delete (This is the BookmarksMenu item)
13) If you poke around in this file, you will notice the History, RSS feeds, and your top level menu that you created in #5.
14) Save the modifications and close the Bookmarks.plist file, (save changes if prompted).
15) DO NOT LAUNCH SAFARI (just a reminder)
16) Launch iTunes and select the iPhone, DO NOT SYNC IT YET.
17) Select the info tab, and scroll to the Web Browser section and select the "Sync Safari bookmarks" checkbox.
18) Scroll to the Advanced section and select the "Bookmarks" checkbox.
19) Click "Apply" and "Sync"
20) wait for sync to complete.
21) remove iPhone from cradle and check your Safari bookmarks. You should be good to go with the iPhone's Safari and its bookmarks, however you are not done yet.
22) THIS IS IMPORTANT. For this modification to last, you have to go back to iTunes.
23) reinstall the iPhone on the cradle, AGAIN DO NOT SYNC.
24) go back to the "Sync Safari bookmarks" checkbox and unselect it. Then click the "Apply" button again. This will prevent Safari on your computer from syncing to Safari on your iPhone. If you ever do, with this box checked, those two pesky menus will reappear.
25) You are done.
Quelle:
Apple Diskussions Forum
(Quellenangabe deshalb, damit nicht die schlauen Füchse wieder irgendetwas denken, was gar nicht ist...)