We strongly recommend to not sync your iPhone, iPad or iPod in iTunes until after you are done transferring all of your iTunes media with iExplorer. Syncing in iTunes will delete any data on your device that's not yet in iTunes, so be sure to cancel any of those iTunes prompts, and to block iTunes from syncing without warning, you can go into iTunes Preferences > Devices tab and check the box to "Prevent iPods, iPhones, and iPads from syncing automatically".
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