iTunes won't backup my iPhone Apps, after iOS 9

Qwian wrote:

it is very bad that we lost our apps in iTunes even in last up date you can not find in left side as normal and nobody can give a good reason

The reason is that Apple removed that feature from iTunes.

Changes in the new iTunes - Apple Support

I have the same issue , i updated to the latest version of iTunes i.e 12.3 and also to the latest iOS 9 and not even my single app was restored by iTunes . I am very angry with this major issue. I had to download all the apps again in my iPhone.

Hi, I think that this is due to a new feature called App Slimming.

With iOS 8 and prior all app binaries were the same. So if you had a universal app (the ones marked with a + in the App Store and say "This app is designed for both iPhone and iPad) and you have both an iPhone and an iPad, the app binaries installed on both devices are exactly the same.

This is all fine and dandy, but when you have a bunch of Apps on a device that doesn't have much memory, having code in my apps on my iPhone that is only needed for the larger UI and features of the iPad or when going the other way apps on my iPad that have code that only runs on the iPhone (or even Apple Watch) it really starts to chew up precious storage space.

It is kinda like when the Intel Macs came out and Apple and other developers offered what were called Universal Applications. A single application bundle that contained the code for both PPC Macs and Intel Macs.

But just like in the iOS case the Universal applications on the Mac took up a lot of extra storage; sometimes hundreds of megabytes. So utility developers came out with tools (like Xslimmer) that would strip out the PPC (or Intel) code from an application and thus make it an Intel (or PPC) only application thus regaining that wasted space because the only time you would need this is if you had an external drive with applications that moved between a PPC Mac and an Intel Mac.

iOS 9 and iTunes 12.3 try to do the same as these utility developers. Now, when you download an app over the air to your device, and the developer has updated the app with this ability, only the iPhone or iPad (or iPod Touch) binaries are downloaded to the device. The rest of the un-needed code is stripped out. What you get are apps on your devices that do the exact same thing as they used to do but are now smaller.

Jump to the iTunes 12.3 back-up issue. When you sync your iPhone (or iPad) to the computer it correctly doesn't download the apps grabbed over the air on your iOS device. This is because the App would only be a partial binary, one that only runs on your iPhone (or maybe even a particular model of iPhone). If you had other iOS devices (like an iPad) and then tried to transfer an app from one device to your computer via iTunes and then to a different iOS device, it probably wouldn't run or would be missing features specifically designed for that device. When you sync a universal binary to your iPhone under iTunes 12.3 it is also doing the stripping of the un-needed code to slim the app. This is why we are required to have 12.3 for iOS 9 devices as prior versions don't know how to do this app slimming.

When you back-up your iPhone to you computer under 12.3 I have been lead to believe now happens is that the slimmed version of the app is also included in the back-up. So if you were to do a restore, even though your apps are not in the App section of iTunes, it will still restore them to your iPhone (or iPad).

If you do want to keep a copy of the full binaries on your computer (iTunes) what I would recommend is going to the iTunes preferences and click on the Store tab and put a little check mark beside "Apps" under the Automatic Downloads section. That way when you purchase an app on your iPhone the full universal binary is automatically downloaded to your computer and ready to be used (and slimmed) for your iPhone or iPad (or iPad Pro). I figure that if a user has the full universal binary in iTunes that when a backup of your device is done, the slimmed version of the app isn't included as part of the backup.

Hope that helps clarify why this is happening. I think in the end we'll be happier to have to extra room to record a few more minutes of our son's first birthday party or first day at school.

Cheers, Andrew.

This would make more sense if the app download on the device wasn't full download. E.g. Pages app was updated to version 2.5.5 (build 1766). So the iDevice decided to download all 600 MB of it, so if it download entire app, why do I have to download it again?

If it only downloaded the delta, I could understand how it can't apply the delta to the version stored on the computer. So, there is still a problem here, even if your hypothesis is correct.

It looks that from now on you have to manually update the apps in iTunes. Basically navigate to the apps page in iTunes, click on Updates at the top and download all full (as in entire app file) updates.

This change makes a compelling case for never downloading updates on your iDevice if you also want to backup to computer. Just download once in iTunes and push the updates to the iDevices during sync.

This is especially the case if you use multiple devices, since in multi device case, each device will download delta update, and then you will have to download full app update in iTunes anyway if you ever intend on restoring your device from backup.

If you never sync to iTunes or are backing up to iCloud, then continue updating only on iDevices.

@Andrew, I have one clarification. iTunes now doesn't backup apps at all.

I installed iOS 9, and then downloaded my all imp apps from app store in order to perform a clean install. But post iOS 9, My iPhone call continuity stopped working and after few failed attempts, I decided to re-fromat the entire iPhone. But before reformatting, I took an encrypted backup of my iPhone. Then I reformatted and set up my device as new. Went to iTunes and manually installed my apps. Guess what happened, all installed apps were older and they all required update. Until now i couldn't figure out why they all needed updates when i backed up those iOS 9 apps few mins ago?

Bottom line: Apps won't get backed up in iTunes anymore.

What @MarioGrgic says is exactly what I did already. I figured that auto app updates in iPhone or iPad won't help anymore if I want to restore my device through a computer. So I have updated my all "Universal" apps in iTunes and now synching them to my devices, with a belief that they will only pass on sliced app. This is classic . They give one functionality which is nice but with a huge side effect.

 can actually make our lives easier if iTunes can automatically create a device specific folder in "Mobile Application" folder in iTunes Media. When we request iOS upgrade via iTunes, it stores device specific iOS firmware in different folder, then why not use the same strategy here? Sure there will be more than a one set of our apps but these would be sliced apps so would take lil lesser space i guess.

Conclusion: The ease of backing up apps in iTunes is gone. puffff...

@Birju, yup that's basically what I said, Apps I don't think will get automatically synched back to iTunes.

Couple questions…

1. did you try going to File > Devices > Transfer Purchases from "device in question" before you formatted your device?
2. you said you made a back-up of your device, set it up as a new device and then manually installed your apps? Why didn't you format your device and then do a restore?

I mentioned that what I think is happening is that when you do a back-up of your device if the full versions are not already in iTunes it backs up the Delta (slimmed down version) in the actual back-up itself. So if you wanted to have the updated apps (if you didn't update them already and separately with iTunes) you would have to do a restore after you formatted your device as a new one.

Anyway, it's still pretty early and we'll get this all figured out sooner or later.

Cheers, Andrew.

I'm thinking that even though the Pages that you downloaded to your iDevice was the full universal app, in the future versions it won't be and iTunes might not know if its a delta version or not. So I'm thinking that from now on iTunes is just assuming that all apps downloaded on iDevices are going to be delta (slimmed down versions) and thus won't download it because there is now no guarantee that the same binary will run on your other iDevices. Soon more and more apps will offer App Slimming, and why wouldn't they?

So the bottom line is that if you continue to sync with your computer and you want to maintain a local copy of all of your apps, you're going to have to download it to your computer to ensure that you have the full universal binary to deploy on your other iDevices.

Which is why I suggested the Automatic downloading setting in the iTunes preferences under the Store tab.

Cheers, Andrew.

Thank you for explaining this, I was beginning to get very frustrated.

You're exactly right, Andrew. I was on the phone with Apple tech support for about 5 or 6 hours and this is exactly the way that they explained it to me. I was even escalated to the most senior engineer advisor who explained this to me exactly the way that you put it in your post. He assured me that everything is backed up. It's just the new way of doing it.

Hey Andrew!

I am using Iphone 5s and Ipad mini. I usually update my apps via iPhone if they are not too big. I connect my iPhone to PC and backup my apps to PC. So PC is my backup for the apps and stuff. I mean i download every single app once and i copy them to other device which doesnt have.

What i understand there are 2 types of apps now (Or will be soon). Universal and Delta. Updated apps over ios device delta and updated apps over pc universal.

If i update an app over ios device, itunes won't backup it to pc cause it is delta. So I have to make all app updates over PC and sync in order not to download them twice right?

I'm totally confused. I wonder if those of us who are older will end up using those old-folks-giant-button phones?!? It seems like they're piecing us right out with each update. 😟

Hi all

My situation is similar to the original post on this thread except I have multi logins using multiple devices. I created a backup for my iPad in my Mac User Account (computer login) under iOS 8 and when backing up got prompted to copy apps and iTunes automatically created a Mobile Applications folder under iTunes Media. Since the update I created a new user for my kids and wanted to restore from backup my daughters new iPad from my son's iPad backup. When running the backup step 5 "copying purchased/copying apps" takes about 2 seconds. No mobile Application folder was created under iTunes Media. When restoring my daughter's iPad from backup, all 100 apps were downloading from the app store through the iPad, which took about all day to do and had to be monitored because the apps became stuck at certain points. I would love to be able to do this through iTunes. I tried to Transfer Purchases from "device in question".

Any suggestions?

Would I be able to organize a master template in iTunes and sync the kids iPads at once?

If this is the case, they should have warned about it. I've several apps that have been removed by the AppStore during the time, but still I have in my library. This way, unless I download them from iTunes and only then syncronize my iPad and iPhone, I wouln't be able to have a backup copy of the same.

So to confirm... The "update" feature in the iTunes program, while still there, no longer works.
Apps no-longer need to be stored on your computer, and can be deleted, since iTunes will no longer look for them - the apps will be stored in the backup file.
At some point in the future, Apple will realise this, and remove the "update" part of iTunes so people don't spend hours trying to work out why iTunes won't bloody update the apps, even though it appears to be trying *flash message of "updating XX app" then cancelling the operation*.