Apple...Please Inform Us and Genius Bar Techs about App Thinning Effects on iTunes Sync!

I thought I’d see if someone could please set the record straight regarding the effect of app thinning in iOS 9 on syncing apps in iTunes. Is it true that apps will no longer be copied to the Mobile Applications folder when syncing an iPhone running iOS 9 in iTunes? And, if this is true, has Apple been forthcoming about these changes, or have they not said much yet? I’ve searched through Apple support publications, tech notes, and so on, but haven’t found any definitive mention of this change.

Case in point. Although I sync and back up my iPhone in iTunes every few days, I noticed a couple of weeks ago that no .ipa files in my Mobile Applications had been updated since September 12…a few days before I updated my iPhone 5s to iOS 9. I also noticed that some of the new apps that I had installed or updated since September 12 didn’t appear in the Mobile Applications folder either, so I thought that was a little strange. Normally I don’t keep an eagle eye on the Mobile Applications folder, but my new 6s was on the way and I’d be setting it up using a backup from my 5s, so I just wanted to make sure that all my ducks were in a row. Thinking that there was something wonky with app syncing in iTunes and that it might be worth trying to sync all of my apps from scratch, I deleted all of the .ipa files in the Mobile Applications folder, then tried using the File > Devices > Transfer Purchases from [my iPhone’s name] function in iTunes. However, no apps downloaded from my iPhone when I selected the “transfer purchases” function. I eventually restored all of the .ipa files I had deleted back into the Mobile Applications folder. Additionally, I noticed that any apps I had installed after upgrading to iOS 9 weren’t appearing in my phone’s apps list/library in iTunes (the list of apps to the left of the "home screens" window in iTunes). I thought this was strange, but hoped it would’t cause problems when restoring my 5s backup to my new 6s.

So I received my new 6s and uploaded a 5s backup that I had made earlier in the day. Overall, restoring the backup to my new 6s went fine. All of my music, photos and data transferred over without any problems, and most of my apps transferred over as well. Surprisingly, all of the apps that I had installed on my 5s after the iOS 9 update had transferred over to the 6s as well, even though they weren’t backed up in the Mobile Applications folder, nor did they appear in my list of apps in iTunes. However, there were about 20 apps that, for whatever reason, didn’t carry over from my 5s. All of the missing apps were present in my list of apps in iTunes, but they did not upload to my 6s. I was able to manually re-download all of the missing apps from iTunes, but any thoughts on why these apps may not have uploaded to my 6s, even though they were in my list of apps and presumably in my library?

Luckily, it didn’t take long to get my new 6s up to speed, but now that I’ve had a chance to create an initial backup of my new 6s in iTunes, I noticed that any apps I downloaded to my 5s after the iOS 9 upgrade (and are now on my 6s) are still not showing up in my list of apps or app library in iTunes. That said, even if it’s true that .ipa files are no longer being copied to the Mobile Applications folder as part of the sync process in iTunes, shouldn’t these apps still be appearing in my list of apps in iTunes? And even though these apps installed after the iOS 9 update don’t appear in my list of apps in iTunes, how did iTunes know to install the apps when I uploaded my 5s backup to the 6s? It would be great if there was a way to re-sync iTunes with the apps actually installed on my 6s, but syncing or using the “transfer purchases” function doesn’t seem to do the trick, and I don’t know of any other way.

On a side note, shortly after I updated my 5s to iOS 9 and first noticed that newly downloaded or updated apps weren’t showing up in my Mobile Applications folder and that newly updated apps weren’t appearing in my apps list in iTunes, I stopped by my local Apple Store and spoke with a tech at the Genius Bar. The tech was about as mystified as I was and wasn’t able to offer any real explanation or solution. At that point, I didn’t know much about app thinning but had seen it mentioned in a few articles I had read about iOS 9. When I asked the tech if my issue could be due to iTunes app syncing being handled differently with iOS 9, he didn’t seem to be aware of any changes and didn’t think that this issue was due to my recent iOS 9 update. If it turns out that what I noticed is, in fact, due to app thinning and changes in the way iTunes syncs apps, then I certainly hope Apple makes its Genius Bar techs aware of this change. I realize that with with iOS 9 and the new 6s, there are a lot of new things for Genius Bar techs to keep up with, but I hope the word gets out regarding these changes, as I’m sure they’ll be getting plenty of inquiries about this issue!