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When I bought my iPad 3 I restored the backup of the iPad 2. As far as I am aware I did not lose any data, side loaded or otherwise. I'm pretty sure an iTunes backup, and I mean a backup you make via iTunes with the iThingie connected via USB, is a full backup. In fact, again AFAIK, it's the only way to back up all the data on your iThingie. That's why I haven't activated cloud backup, although you can still make a manual iTunes backup after activating the cloud backup.
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