How can I get iTunes to recognize my iPhone 4S again without having to re-configure all my apps?

I have an iPhone 4S that I have bought directly from Apple. I used iTunes on my very old (2006) Mac to set it up and do the initial sync. After that, I did an OTA firmware update and several OTA syncs without problems. I also set it up to perform iCloud backups. When I next tried to connect the phone to iTunes about a week later, the connection felt rather flaky (the phone appeared and disappeared a few times), so I ran the recommended iTunes update.

I reconnected my phone, and iTunes greeted me with a "Set up your iPhone" screen, which offered me the choice of "restoring from backup" (to my knowledge and from the dates offered, this only refers to the backups iTunes has made, not iCloud), and "setting up as a new iPhone" or something to that end.

I did some research and found that some people had that same problem, but said it went away when the allowed it to set up as a new iPhone, which, as they said, would do nothing and everything would be good afterwards. Well, they were right that it did nothing to my phone, but now all those checkmarks ("sync music", "sync contacts", most importantly: "sync apps") are unchecked. If I re-check any of them, the program makes it quite clear to me that first, everything on my phone will be wiped, and then being installed as instructed. I.e. if I did this with my apps, I believe all my settings would be lost and I would have to set all of them up again.

I even went to the "Genius Bar" today and explained all this. The answer was this: reset your iPhone to factory settings, connect to iTunes to make it recognize it again, then restore from iCloud (where both all app settings and the screen layouts are stored).

Sounded reasonable back there, but when I tried this, I found this little problem: You can only restore to a fresh device from iCloud, but iTunes will either want to set it up for me first (so it's no longer fresh after that), or, if we do an iCloud restore, it goes back to showing me the settings with all checkboxes unchecked.

Maybe I just overlooked one crucial little detail, but I don't see it, so...

what can I do to remedy this?

I know the easy way out is to just wipe the phone and install again from iTunes, but what bothers me is that this disconnect can happen to me again and again - I don't want to wipe my phone and reconfigure all my apps every time this happens. So that's why I'm looking for the "right" solution, rather than the "quick and dirty" one.

Solution 1:

Coincidentally, that happened to me just one week ago when Wifi sync died en route. The solution is simple, but totally non-intuitive: do the exact opposite of what feels right, and all will be well (not exactly Apple’s finest hour in UI intuitiveness):

1. Choose “set up as new phone” on the initial screen. In the dialog that pop ups give your phone the name it had before (important – if your case is similar to mine, it will be pre-filled). This will re-register the phone with iTunes sync.
2. Your phone will do an initial sync with all sync options (music, movies, ebooks etc.) disabled except apps, which are set to “sync all” (if you have a lot of apps in iTunes you are not usually syncing to your phone, the initial sync will flood your phone with these. Delete them out of iTunes beforehand, or from the iPhone after the initial sync). Apps already on the phone will not be overwritten and won’t lose their settings.
3. At this point, all media will still be both in Tunes and on the phone, but not in a synchronized state. Re-check all your sync settings. Acknowledge the “all media on this phone will be deleted” warning. Don’t fret: as long as you are syncing with the same iTunes library as before, nothing will be deleted in the next step.
4. Trigger a sync manually. iTunes will compare what is on the iPhone and what it is meant to sync, and will not re-transfer media already on your phone. Once done, both media libraries will be in sync again. One gotcha though: make sure the downsample setting on the first option page is set as it was before (i.e. on if you downsample music to 128 Kb/s in sync, off otherwise), or you music will be re-synced because bitrates do not match – quite a pain if you have a large library.

After that, your phone will be back ins sync without undue hassle (i.e. worrying about out of date backups in iTunes, iCloud restore etc.).