Set up new iPhone 5 with iCloud restore, then iTunes created new library with only content already on phone. How do I find and sync everything in original library?

My daughter got a new iPhone 5 and we set it up using the option to restore her iPhone 4 backup from iCloud. This worked great and everything on the old phone showed up on the new phone. Because we were traveling, we weren't able to sync the iPhone 5 with iTunes at that time.
She purchased new apps and music on the iPhone 5. When we returned home she synced with iTunes, and it seems to have created a new library, with only the content currently on the phone. I don't know if it prompted her to do this on the first sync or not - she doesn't remember.
So in iTunes, the library now only shows the music on the phone. A sync isn't doing much now because when choosing the phone in iTunes and selecting each content type across the top (Apps, Music, Movies, TV Shows) the box is unchecked to sync that content. When I check the box to "Sync Music", iTunes gives a warning:
Are you sure you want to sync music? all existing songs and playlists on the iPhone Becca's iPhone will be replaced with songs and playlists from your iTunes library.
Same goes for apps, except that warning also mentions that the apps and their data will be erased and replaced.
At some point she was also getting a message that this iPhone was associated with another library, but I'm not sure how she had triggered that. She says she canceled out of that. I can see all of the music
How do we get iTunes to see the "old" library of songs, videos and apps without losing the ones she's purchased already on the iPhone? The music files themselves are still on the computer, and include music both purchased from iTunes as well as music ripped from CDs. Thanks for any advice!

See Recover your iTunes library from your iPod or iOS device.
tt2

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