Q: iOS 9 updated apps won't copy to iTunes

This is true. Because of app thinning, iTunes now refuses to backup apps which is an absolutely horrible option for 90% of  users because during any reformatting event, we have to download that each and every app again using our data plan. This is insane. App thinning is nice, it may have cleared some space in our iPhones but guess what, our data bills are going to be huge now on. and even if we forget about this data usage, the time it takes to download all the apps is insane. My iPhone 6 became oven while updating 43 apps last night!

A simple solution may just work fine if  changes only one thing. Until now all the apps were getting backed up in "Mobile Application" folder irrespective of the devices. iTunes just needs to create different folders for different devices under "Mobile Application" and all the relevant sliced apps get backedup in those device folder. This type of device specific folders already there when we request iOS update through iTunes. Wondering why can't we have the similar function for backup? we all have 500 Gb to 1 TB hdd in our mac and pc. sure we can handle few gb of data storage than this data charges.

I found an article about IOS 9 ...  :

http://www.imore.com/ios-9-review?utm_medium=slider&utm_campaign=navigation&utm_ source=im

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... in which I learned that at least for NOTES, thorough synching will only occur between an IOS 9 device and a Mac running OS 10.11 El Capitan.

Here is an exerpt :

Notes is still synced using your iCloud account, so if you have an iPhone and an iPad or Mac, anything you note down on one will show up on the other or others. The new versions are different enough, however, that you can only sync iOS 9 with OS X El Capitan and vice versa. So, if you want to use Notes, you'll need to go all in on all your devices. This presents a temporary dilemma for Notes users: OS X El Capitan isn't due out until 2 weeks after iOS 9.

I wonder if our problem with purchased apps on a device not synching with iTunes doesn't simply arise from the fact that our Macs are still running Yosemite.

Has anyone tried to sync an IOS 9 device with El Capitan yet ?

YM

This will result that I need to download all apps from Internet if I am restoring my phone !!

Very smart  move from Apple

Just make sure you update your apps on your computer rather than your device and sync them over.  Back up the mobile apps folder in iTunes media from your computer to a back up hard drive regularly so if your phone should need restoring everything is there.

I'm just having to remember that there's no point downloading any app updates on my iPod Touch or iPad because they won't transfer over purely because my broadband can end up slower if I overdo the data download.  So far as my iPhone is concerned, if when away from home an app needs an update due to a bug or has better functions then I'll use my phone data to download but will still have to download on PC to add to my other devices.

It's only a concern to people who have a limited broadband package or where their service provider is quick to slow the broadband down if a lot of data is used.  I guess it makes sense for those who get the lower capacity devices where space is at a premium, as I have 128 Gb on mine I had no problem if app sizes were bigger than they needed to be.

i am also having the same issue.Is it just me or is apple really starting to go downhill. I used to trust apple to a certain degree, but now they seem to rush out software and hardware with bugs and problems just to make a quick few quid. I am sure like me people will really start to resent apple and there shortfalls.I certainly won't be buying anymore apple products because i am just sick of the problems.

iOS 9.0.1 does not fix the Problem. Maybe is it really a Feature?!

This bug is extremely annoying. I end up updating the same app more than once if I do it on the iOS device as iTunes will download it again.

Also found that if one copies a PDF to iBooks on the iOS device, it will sync it back to iTunes every time the devices are synched.

This is quite a bizarre change from Apple and is obviously designed to shift users further towards iCloud.

I usually download all my apps via my phone and then transfer them to iTunes for backup purposes. My understanding is that when you restore your phone from an iCloud backup your iCloud backup doesn't actually contain copies of your apps, just a link to what you have downloaded and then during the iPhone restore process they are re-downloaded from the app store. BUT what happens to apps that are no longer available in the app store, if they cannot be transferred to iTunes then essentially we lose them...unless every time we download a new app we also download it into iTunes separately?!

I noticed last night that LastPass and Twitter had not updated.  I got it to work, after a lot of other tips failed me, by doing this:

1. Started ITUNES with the phone hooked up and set to sync over the cable, not wifi.  Disconnected the phone.
2. Went to the apps section of the ITUNES Store. Clicked Updates, scrolled to the bottom of the rather extensive list (since I'd never updated on my pc before), and opted to Update Everything.  Updating all the apps took quite a while; the apps needing updating disappear from the list as the updates occur.  When it is empty, the pc's apps are all updated.
3. Hooked my iphone.  It would not synch, ITUNES said it could not find the phone.  Changed the name of the phone, and hooked it up again.  ITUNES found the phone okay.  I'm not sure why all that happened, maybe because a tip that didn't work said to reset all the settings on the phone?  Dunno.
4. Synched the phone to Itunes.  The updated twitter and LastPass apps loaded to the phone, replacing the "old" versions.

I found that it is a bit different.

1. If I download updates on my iOS devices, it does not synch the updates back to iTunes
2. If I download the updates in iTunes, it syncs to the iOS devices
3. I have noticed that there have been pending updates on the iOS device but they do not appear as updates in iTunes unless I go to the specific app and then it has the update there but not in the Update section in iTunes.

Seems to me that despite the comments about different versions of updates, this is not the way it should work. In particular, if you update on the iOS device, it should sync back up and all updates should appear in the Update section in iTunes. This clearly does not work as one would reasonable expect. Its broken.

Agreed. I'm sure many people update their apps via their iPhone or iPad when they are away from their computer and then sync back to iTunes. It was a great way to maximize a mobile data plan vs. a home plan. Now the contract data plan on the phone will be under-utilized while some of us that are "capped" at sizes at home will face higher costs. The work-around could be to create a hot=spot on the phone and download updates on the computer, but I live in a rural area with lousy cell coverage. Plus, isn't this a step backwards to "ease-of-use?" I understand the app-thinning idea but there should be a couple of options (aka choices) here.

I think I may have resolved this error as I had the same issue too.

Click on the face icon near the search bar in iTunes, then click on Purchased. Highlight the tab not in my library and there should be an option to click download all. This should have all the apps that have been purchased put in to your library.

I hope this helps others too.

Just what we need, more confusion.

I found a few there under "family purchases", and also by checking for items not in my library by checking both my downloads and those for my wife.  Maybe a part of this overall problem is the new family sharing feature