Hi inywil,
Thanks for using Apple Support Communities. Is it possible they were purchased under a different Apple ID? You can use this article to locate any other Apple IDs you might have:
Apple ID: Finding your Apple ID
http://support.apple.com/kb/HT5625
Additionally, you might be able to find out which account was used to purchase the missing items by looking at the 'Get Info' screen of items you still have:
Recovering a forgotten iTunes Store account name
http://support.apple.com/kb/ht1920
If you're able to locate the account they were purchased with, you can use the steps in this article to download them again:
Downloading past purchases from the App Store, iBookstore, and iTunes Store
http://support.apple.com/kb/ht2519
Cheers,
- Ari