Currently Being ModeratedNov 13, 2012 5:33 PM (in response to Pinksteady)
Ok I've found the answer, and it is nuts:
1. On iTunes apps tab, uncheck the sync apps tick box if its already checked. This then previews the current iphone page layout (may have to quit and re-open iTunes).
2. Check it back again (it will look like its going to remove all apps) then click on the apply button to start syncing.
3. However, even before the syncing takes effect, click the cancel "x" button on the status window found on the center part of iTunes where it displays the sync progress.
4. Restart iTunes.
5. Voila - iTunes has magically inherited all the apps and folders on the phone.
Currently Being ModeratedNov 13, 2012 5:37 PM (in response to Pinksteady)
Follow the steps here: https://discussions.apple.com/docs/DOC-3141. If you aren't syncing your calendar or contacts with your computer you can skip step #2 (just be sure these aren't selected on the Info tab of your iTunes sync settings befor you sync). You'll still need to uncheck the apps in iTunes you don't want on your phone but your app/folder layout should be preserved.
Currently Being ModeratedNov 13, 2012 5:58 PM (in response to Pinksteady)
I've been complaining to Apple for the past month or so regarding this behaviour. Like you, I was adding apps directly to the iPhone using the App Store instead of syncing. The truth is, there's no way around it. At least, no way that doesn't make you facepalm yourself into the last century.
The solution was recently presented to me during an iPhone replacement process through AppleCare:
1) Make a backup of the phone to your computer through iTunes. NB: It may not be necessary that the backup is on your computer, as opposed to iCloud; the process I'm outlining here is what worked for me, and I'm reluctant to advise outwith what I've directly experienced.
2) This is VERY IMPORTANT: back up the backup you just made, possibly to several places. You can find it at /Users/<username>/Library/Application Support/MobileSync/Backup/. Back it up by simply dragging-and-dropping the appropriate folder to a new location—or two (make sure you don't move it instead). If you have more than one device's backups on your Mac, you should be able to determine which belongs to the iPhone 4S by Get Info… on each folder here, and seeing which one has the most recent Last Modified time.
2) Right-click your iPhone in the iTunes Sidebar and choose, Transfer Purchases From iPhone.
3) Right-click again on the iPhone and choose, Reset Warnings.
4) Restore your iPhone as a new device. If prompted to restore from a backup when this process completes, choose No. If prompted to make a backup, choose No. Regarding the latter, you may find it doesn't ask, and simply makes a new backup anyway. That's what happened to me—hence the backup of the backup!
5) Restore your phone from the backup you made.
At this point, no third-party apps will have been restored. If you had any Configuration Profiles installed, they are not restored either. Nor is Music or Videos. All the native apps should be restored, however, along with general settings and preferences, any data they contained, and their Home Screen positions. I was led to believe photos taken with the Camera would not be restored, but they were. YMMV.
6) Now, immediately go to the Apps tab, enable App Syncing and select all the third-party apps that were previously on the phone. At this point, don't add anything that wasn't on the phone prior to being Restored. The apps will appear in order of selection on the iPhone's Home Screen(s), rather than being returned to their previously-assigned positions. It's up to you whether or not you re-position them now, in iTunes, or later, once they've been synced.
Once this process is complete, you should find your phone back in its original state, but with syncing now possible through iTunes. Some apps may not have retained their data: in my case, TVGuide consistently lost all its settings, including my channel selections, and Twitter lost its history of tweets. Also, when I attempted to sync Music I received the same, "your iPhone must be erased" message, so this process doesn't appear to be the panacea we'd like. However, if you choose to sync Music etc. in (6) above, you may find it works. Personally, I haven't tried it, so can't say.
It's late, so I'll stop here. But I think that's complete.
PS: Oh, and put in some Feedback regarding this ludicrous state of affairs