IPhone – The iPhone is synced with another iTunes library error Message

In researching solutions, I found this discussion at apple.com in which somebody suggests "damaging" the iTunes library. This lead to a very useful post which discusses how iTunes uses the data it has to recreate what it doesn't have and gives instructions on how to damage (without deleting) the file -- spoiler: erase the data, leave the file.

Fortunately, I had backed up the iTunes files before I recreated the iTunes library.

I copied my backed up files back into the iTunes directory and launched iTunes and rebuilt what it needed to. There were no apps listed in the Apps display though.

When I connected my iPad, iTunes didn't complain about this being an unknown device. As it started to sync, it prompted my to transfer purchases (i.e. the apps on my iPad which didn't show in iTunes) -- but with no hint of having to erase anything. The sync took longer than normal, but everything is there and I can even find the songs which were originally hidden.

iPad is fine, will sync my wife's iPhone tonight.

The solution is a two part solution.

If you routinely want to sync one device with two libraries, the easiest manner is to disable all automatic syncing on the first iTunes library before you bring the iOS device to the second computer.

You can always wait for the "erase" warning and cancel the sync. (which is the point you have in your screenshot). At that point, go into the current device settings and turn off automatic sync for all of the categories that cause the warning dialog to appear. Keep in mind, that music, ringtones, and other settings can all get the warning to pop up, so your work may not be done by simply un-checking music. The settings on the computer you get the warning are in conflict with the settings from the previous computer so you have to reconcile that before the manual sync can start.

Once you have figured out all the "silos" that matter to you, you can easily take one device to multiple computers for backup but only certain computers for syncing. Using one computer to sync the data (contacts and calendar) and another for the media is a use case that Apple fully supports in iTunes. Once you set things up, you should not expect to have issues with a one device and many computers situation.