Apple appears to be working on a process to allow iTunes users with more than one Apple ID to somehow "merge" them into a single account. The ability to do so will be critical to the early success of the company's new iCloud service, since it relies on Apple IDs for syncing iTunes purchases and other data.
The problem with managing multiple Apple IDs with iCloud first became apparent when Apple launched an early beta of one of its features called "iTunes in the Cloud." It allows users to automatically sync iTunes purchases between iOS devices and computers running iTunes. When you link an Apple ID to your iPhone, for instance, any apps, songs, and iBooks you buy from your computer are automatically downloaded to your iPhone (and vice versa).
The problem comes in when users have multiple Apple IDs. Users may have multiple Apple IDs for a variety of reasons, such as separate accounts for work and home use, or multiple Apple IDs used by a single family. MobileMe users can also use their MobileMe accounts as an Apple ID. Most MobileMe users likely had Apple IDs before they had MobileMe accounts, however, so all these users effectively have two Apple IDs even if they don't know it.
If you started using your MobileMe account to log in to iTunes for App Store or other purchases, older purchases are still associated with your older, original Apple ID. That's not a problem on your computer—you can have multiple iTunes accounts authorized on a Mac or PC. Unfortunately, you can only associate one Apple ID with a particular device in any 90-day period for iTunes in the Cloud. If you were hoping to sync both work-related and personal iTunes Store purchases to a single device, for instance, you're currently out of luck.
The problem could get far worse once iCloud launches, which is expected to happen in the next few weeks. iCloud will effectively replace MobileMe going forward, and existing MobileMe users will be able to convert their accounts to iCloud accounts. But if you associate that iCloud account with your device, you won't be able to access all the songs and other data you bought using a separate Apple ID. One developer currently testing the full iCloud beta confirmed to Ars that juggling the two accounts causes issues with iTunes syncing, and in some cases songs are disappearing from the library on his device. This has been independently confirmed by other developers as well.
Currently there is no known workaround. Apple IDs "cannot be consolidated," according to Apple, and it's not possible to change your current Apple ID to match your MobileMe account (trust us, we tried). Keep in mind that Apple has stated that you can still convert a MobileMe account to iCloud but use a different Apple ID for iTunes-related syncing. As long as you have only used one Apple ID for iTunes purchases, you should be fine. If not, there could be trouble.
The good news is that Apple definitely seems to be working on a solution. At least two MacRumors readers that have e-mailed Apple's newly appointed CEO Tim Cook about the problem have received phone calls from Apple employees acknowledging the issue. Apparently the team responsible for Apple IDs is aware that users are frustrated, and is working on a way to combine accounts or associate multiple Apple IDs with a single device.
Apple was not able to respond to our request for more specific information on the Apple ID issue, but we suspect that coming up with a workable solution is a top priority. If the problem is still present at the time of iCloud's launch, Apple runs the risk of another customer service disaster on the scale that accompanied the botched launch of MobileMe in 2008. Problems syncing contacts, accessing e-mail, and other frustrations chronically plagued MobileMe users for the first several months, ultimately resulting in Apple offering as much as six months of free service for early adopters. A major iCloud syncing headache won't help the perception that cloud services in general, and Apple's in particular, are inherently untrustworthy.
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