iPhone 4S - backed up and transferred purchases, but says I will have to repurchase

Following a call to Apple support, I need to restore my iPhone to factory condition to test for a fault. I therefore carried out a backup (on a computer that had never been synced before - I turned off auto-sync, and the back-up is fine). I authorised the computer, and told it to transfer purchases from my device, which it did. But when I tell it to 'Restore iPhone' I get a warning that I have purchased content on the phone which is not backed up and which I will have to repurchase! So how do I back up those purchases?

Thanks,

Helen