Where are iTunes sync settings stored?

After upgrading to iOS 6 on my iPhone 4, the sychronization settings it iTunes appear to have been reset on my Macbook Pro. Another strange thing about this "reset" is the only settings affected were those for Music and Video.
I had updated several apps on the Macbook and needed to sync those apps to my iPhone, as well as a couple purchased on the iPhone since my last sync with the Mac. So ... I connected my iPhone to the Macbook, and after reconizing my phone the "Sync" button became activated. Since I was on the Summary page, I suspected no changes, as I had made none, and the Capacity bar was full to about .2GB Free, as expected. I pressed the "Sync" button as usual.
Somewhere between steps 1 and 2 (or during step 2), the Capacity bar dropped to Green, Yellow and a sliver of Orange with 23.2GB Free?!? Whassup?? As there was no method (I am aware of short of powering down the laptop) to pause/stop sync in progress, which I suspect would be dangerous anyway, I was forced to let it complete. After it finished. I checked my iPhone and the music and videos had all been removed. When I examined the sync settings in iTunes, I noticed the Sync Music and Sync Movies check boxes were selected. All other check boxes below them for Music: Playlists, Artists, Albums, Genre, Include music videos; and Movies: Movie Names, had mysteriously been unselected.
Since all my files are still in the proper folders on the Macbook Pro, and I use Time Machine, I am not concerned about file loss. What I am concerned with is how did this happen and where are these settings stored, so I do not have to go through ehem all and reselect each and every one to prevent this from recuring in the future. The technician and his manager could not find the location of these settings, as we tried replacing an older version from Time Machine to no avail.
Could anyone please tell me where the Synchronization settings in iTunes are stored, so I might be able to recover the proper file and not have to reselect each sub-selection to return my music and videos to the iPhone? I can Restore my iPhone from the backup just prior to the Sync; however, these does nothing to prevent the incorrect iTunes Sync settings from removing my music and video next time to transfer/sync upgraded apps.
Thank you in advance for your assistance. For more details see below regarding OS, iTunes and iPhone versions.
Sincerely,
Wynne Hunkler
OS:          10.7.5 (Lion)
iOS:          6.0 (10A403)
iTunes:     10.7 (21)

I think the device stores those selections along with which library they belong to. That's why you get the prompt to erase and reload with a different library. If you had restored the backup taken immediately before the upgrade that would probably have restored your selections.
tt2

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