The itunes route only works the other way around.
No idea where you got that idea... It works both ways. Just make sure you have at least one entry in the address book you want to sync with on the computer. If you don't, then the contacts on the phone will be erased. If you do, then you will be given the opportunity to merge the contacts on the phone with those on your computer.
You tried this?
You can sync contacts, calendars, bookmarks, and notes with other applications on your computer. This allows you keep all your information in sync across multiple computers and iOS devices. The settings for these items are all in the Info tab for your iOS device in iTunes. With your iOS device connected to the computer, select your iOS device. Then click the Info tab.
For details on syncing content on your iOS device with your computer, click the sections below.
To sync contacts with your computer, choose "Sync Contacts with" within iTunes for Windows, or "Sync Address Book Contacts" on your Mac.
You can sync your contacts with:
- Microsoft Outlook 2003, Microsoft Outlook 2007, Microsoft Outlook 2010 (Windows XP, Windows Vista, or Windows 7)
- Windows Address Book (Windows XP)
- Windows Contacts (Windows Vista / Windows 7)
- Address Book (Mac OS X)
- Microsoft Entourage 2004, Microsoft Entourage 2008, or Microsoft Outlook 2011 for Mac
Note: If using Microsoft Entourage, use Microsoft Entourage 2008 12.1.2 or later if syncing with Mac OS X v10.6 or later. If you would like to sync data on your Mac with Entourage, enable syncing between Entourage and Address Book.
- When syncing contacts, you can choose to sync all of your contacts or only selected groups. The option to sync selected items may not show up until after the first sync.
- You can select a group of contacts to which all new contacts created on your iOS device will be added.
- Additional options for syncing include syncing your contacts with Yahoo or Gmail/Google Mail. You will need to configure it with the user name and password for your Yahoo or Google account.
Were the contacts in your phone previously synced with something else? (e.g. an Exchange account that is no longer active)
I had the same problem, most of my contacts would sync, but some wouldn't. Then I realized the contacts that wouldn't sync in iTunes were actually stored in my gmail and they were "push" synced with my phone through my gmail account, not my iTunes or Apple Address book. So I logged into gmail, exported my contacts as cvv file and then imported them into Apple Contacts. Once I did that they synced to the phone.