ISSUE RESOLVED
I tested this out on my ipod first, and it worked, so I did it on my ipad,
and it worked as well
To recap, this process assumes the device has the apps and layout you want, and iTunes does not, yet you want the sync function to work again, like it used to, and leave you with the setup you now have on the device, and become back in sync with iTunes
Process does not take too long at all -- and its much faster that trying to rebuild the layout manually all over again.
Heres what I did. I suggest you read this through once before trying it.
0) Do NOT connect the device
1) Start iTunes. Go to Edit, Preferences, Device backups
2) Select Prevent ipods from syncing automatically
3) Delete the backups listed
4) Connect the device
5) Right click on the device in the left pane, and select Backup
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You now have a good backup, good device, still bad iTunes
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6) Under Sync, it may or may not be greyed out with your desired layout showing.
7) Checkmark the Sync Apps check box
8) Peform the dreaded sync ( this will temporarily leave you with the bad layout on your device . Have faith) .It may ask to transfer purchases back to iTunes, say Yes.It may tell you that your device is activated on another machine and do your really want ot erase thr apps on the device
and sync to iTunes - say Yes. Dont worry - this is temporary.
9) At this stage, the bad layout is now synced to your device (keep praying but it will be ok)
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You now have a good backup, bad device, bad iTunes
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10) Go to Edit, Preferences, Device backups
11) Delete the most recent backup, keep the old backup (the good one)
12) Right click on the device in the left pane, and select Restore from Backup. Let it completely do its thing.
13) Your device will likely NOT be listed any more, but if you look at your device, it has the good setup (because of the restore)
14) Disconnect your device and close iTunes (it may close automatically when you disconnect
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You now have a good backup, good device, still bad iTunes
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15) Start up Itunes
16) Connect you device
17) Under Sync, it may or may not be greyed out with your sesired layot
showing. Checkmark the Sync Apps check box. It will warn you all your
exisitng apps will be repalced. Your 'wrong' layout will again appear.
18) Do another restore
19) Under Sync apps , it will look wrong, but dont worry - close iTunes
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20) Restart iTunes - EVERYTHING SHOULD BE BACK TO NORMAL NOW
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You now have a good backup, good device, good iTunes !!!
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At this point, create another backup - Right click on the device in the left pane, and select Backup
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