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I'm thinking about use Ubuntu's Rythmbox to synchronize music, but I need the iTunes from my windows to get some apps.

If I plug my ipod to a windows with no musics on it (to get my apps), my musics will be deleted from ipod?

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I can confirm what Nathan G. reported. I have a computer with Windows, and when I plug my iPod on that computer, it says me it is already synchronized with an iTune library; it asks me if I want to synchronize it with the library present on Windows, warning me that the content of the iPod will be deleted, if I decide to do so.

I didn't select Manually Manage Music in both the computers.

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In my experience, it asks you. You can say no. However, I'm not sure if this requires Manually Manage Music to be checked in the Summary tab.

As always, make a good backup just in case.

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Go into the Preferences of iTunes. Under the Devices tab, there is a checkbox for "Prevent iPods and iPhones from syncing automatically". Make sure that option is checked and you are in the clear.

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