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I sync my iPhone via iTunes from data stored in my external data. All of my data ( ie, music, iTunes libraries etc) are stored in the external drive.

Now my external drive isn't powering on due to power adapter issues. What I'm wondering, is, if I create a new library and use that library to sync to my iPhone, will my existing content on the iPhone get deleted ?

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If you sync your iPhone with a fresh copy of iTunes it will delete those data in your iPhone. The only solution(in fact the best :) ) solution would be this,

Step1: Download Diskaid [this will let you use your iPhone in disk mode just like iPods

Step2: Change your sync mode to Manually-Sync before connect to your iTunes.

Step3: Run Diskaid and transfer all your music you want to add to iTunes to your computer first.

Step4: Now you would have got your iTunes to what it used to be & you can change sync to automatically & use it as you always would

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Thank,s I'll try this and update. What about my apps ? –  Sathya Nov 11 '09 at 20:22
    
you can use iPhoneexplorer[code.google.com/p/iphonebrowser/] to backup virtually anything u want from ur iPhone. –  Avis Nov 12 '09 at 3:51

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