What does it mean to sync apps to iPhone? I don't understand exactly what this does, or why I'd want to turn it on. What are the advantages/disadvantages of enabling "Sync Apps" in iTunes to my iPhone?
IPhone – What does it mean to sync apps to iPhone
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Related Solutions
It sounds as though your iPhone and/or iTunes aren’t synced to each other. Unfortunately, for you to manage the apps on the iPhone from iTunes, the iPhone needs to be synced to iTunes. So you’ll have to go through this procedure at least once, and replace what’s on the iPhone w/ what’s in iTunes.
No way around that, but thankfully, any apps you’ve purchased are free to you to download again, so if there are any that are missing in iTunes, just download them again.
But yes, if any of the apps aren’t in iTunes, and you’ve got data stored in those apps, that data will be lost.
iTunes will sync photos only if you turn on photo syncing in the "tab" for photos.
If iTunes is complaining about apps, it's likely that you once started to sync apps (or it got confused) - but it has nothing to do with app syncing. Sadly, if you want to use this iTunes library, you have to deal with the app issue or keep facing that alert.
Think of it this way. Your photos are in a room that happens to have some rotten food. You can either move your photos to a new room or deal with the rotten food by holding your nose or cleaning it up. One didn't cause the other, but they just ended up in the same room as you.
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Best Answer
This Apple Support article provides a quick summary of what syncing does. Basically, as XAlexOwnZX mentions, a sync copies applications, music, and other information between your iTunes account and your iDevice. This process backs up the content (apps, etc.) on your computer.
The advantage of syncing is that if your iPhone gets corrupted, you'll be able to restore it (or its replacement) to working condition, with all of the purchased content that is installed.
The disadvantage is that syncing takes time - however, with iOS 5, you can choose to sync over WiFi and you don't need to tether your iPhone to your computer.