Band on the Run: I don't know whether this could be your problem, but my Significant Other had a similar issue with some Kindle books she had bought on Amazon. On her Kindle app, she couldn't find certain books she knew she had bought. They weren't even listed under her Amazon account. We emailed Amazon about her disappearing books and they discovered the problem. It turned out that she had inadvertently used her email address to set up 2 different accounts with the same user ID but with different passwords. She set up the second one when she wanted to buy something and forgot she already had an account. Anyway, the solution was simple. Amazon combined the accounts and she selected which password she wanted to use with the new combined account.
Good luck.