I cant't tell since I do not understand the exact sequence you described.
What you need to do is;
- Make iTunes backup of the iPhone
- Restore the iPod from that iPhone backup
NOTE:
If you restore from iCloud backup the apps will be automatically downloaded. If you restore from iTunes backup the apps and music have to be in the iTunes library since synced media like apps and music are not included in the backup of the iOS device that iTunes makes.
You can redownload most iTunes purchases by:
Downloading past purchases from the App Store, iBookstore, and iTunes Store
- Then you can do what you want with the iPhone.
NOTE
if you restore the iPhone and then sync (the first step of the sync is to backup the iPhone) the previous backup of the iPhone will be overwritten with the canges