During my iPhone firmware update fiasco I had nothing but trouble getting a proper restore of my data. Some – but not all – of the applications would be restored using iTunes 9.

According to a post at Apple Support:

Although iTunes backs up most of your iPhone and iPod touch settings, downloaded applications, your audio, video, and photo content are not included in the backup.

Another post describes what is backed up with each version of the iPhone OS. The following is excerpted specifically regarding applications:

iPhone 1.1

• Application settings, preferences, and data

iPhone 2.0 and later

• App Store Application data (except the Application itself, its tmp and Caches folder)

iPhone 3.0

• Per app preferences allowing use of location services
• In-app purchases

What I’m reading here is that iPhone applications are not backed up in iTunes. This doesn’t explain why some apps get backed/restored while others do not. Nor have I found any backup/restore correspondence if the application was downloaded OTA versus purchased within iTunes.

Fortunately Apple allows you to re-download iPhone applications at no charge but this shouldn’t be necessary if iTunes actually backed them up.

Related posts:

• Problems with iTunes 9 and iPhone restore
• iPhone 3.1.2 problems linked to AT&T carrier update 5.6
• Repaired Mac? Prepare for a licensing reboot
• Tape backup – don’t bet your life on it
• Fixing iTunes authorization for multiple computers