Apple may be working on a way to merge Apple IDs to avoid a big syncing mess when its iCloud launches in October along with iOS 5 and the iPhone 5. The company has long rejected the ability to merge Apple IDs, which is an issue for users that may have inadvertently signed up for more than one. This issue also plagues those who had a MobileMe account.
The Apple ID is what's used to sync and download purchases from iTunes. If a user has made purchases on two Apple IDs, they can only download or sync with one at a time. They also cannot quickly switch between the two accounts because Apple locks devices to a single Apple ID for 90 days. Users who are frustrated with this inability to merge Apple IDs have gotten little guidance from Apple.
However, a MacRumors reader recently emailed Apple CEO Tim Cook regarding the problem and received a phone call from an Apple spokesperson, acknowledging the Apple ID issue, and revealing that although the accounts still cannot be merged at the moment, they are indeed working on a fix. Another reader reported a similar response from Apple. But for the time being, it's recommended to pick one of the accounts and make any future purchases from only that account.