My Purchased folder doesn't restore from Backup disc

I changed my iTunes music to an external drive (following the instructions listed by Jesse Hollington on Transferring your iTunes Library as suggested in a Support Discussion) but later decided I could live with it being back on my internal hard drive.
I have since noticed that not all my purchases are in my Purchased folder. Having recently performed File>Library>Backup to Disc I did a Restore with the Ovewriting option ticked. All my Playlists are correctly showing but only one Purchased file is in the folder. When I play some of my 'Purchased' songs from playlists I had created they play correctly. When I Get Information on the tracks they show up as AAC Purchased songs.
Can anyone assist as to why they do not show in to the Purchased folder?
I am using OSX 10.6.8 and iTunes 10.3.1

Well thanks for your help since you were the only one who commented, but I had already figured it out the next day I had posted this. There were two things wrong. 1: The sales person who went ahead and set-up my phone as a new phone was one thing and a recover had to be done. 2: My internet was down that night for some unknown reason while I was updating my phone, so that caused it to get stuck on that picture that's says "Connet to iTunes", but before that I was using my personal hotspot.
Again, thanks for your help .

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I purchased an iPhone 5 new back in December 2012 Removed it from the box, powered it on and started entering my contacts from my old (non-smart) phone by hand. After done entering my contacts, I then proceeded to setup Messages, iTunes, the App store etc with the Apple ID of my wife's phone since we really don't have a need for separate Apple ID's.
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If any further info is needed, I will be glad to supply it.
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I would like to preface that I have NOT tried what I am about to post.
I came across this forum post that seems to answer the question I originally posted above.
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My Purchased folder doesn't restore from Backup disc

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