My Ipod Shuffle 3rd Gen appears in Windows but not in Itunes

It all Started going wrong when i converted all my music to AAC versions and deleted the old versions so it would work in my car. Since then it won't connect to Itunes but shows up in WIndows. It has taken all of my music off but still charges.
...Help

Have you worked through all the suggestions in this Apple support document?
iPod: Appears in Windows but not in iTunes
B-rock

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