Purchased music not showing on iTunes purchased music list.

My wife is an iPhone user and she has an extensive CD collection that she used PC iTunes to load onto her iPhone. So her iPhone was a mix of copied CD’s and music she downloaded from iTunes A while back she

upgraded her iPhone and the everything copied over to the new iPhone.  Yesterday we hooked the iPhone up to iTunes for the first time. On the first sync iTunes removed all of the CD sourced music.  On the second attempt iTunes questioned if this was the phone for the account. After answering yes, a download initiated that took several hours to complete. Everything seemed fine except for about 17 CD’s that were purchased and downloaded from iTunes were missing.  They were also missing from the iTunes purchased music list. Right now I will be out about $200 to restore music I have already paid for, can anyone please help?