My folders/apps all messed up/missing after upgrade

So I was able to get my music and all other stuff back on after the upgrade (they didn't work right off). Now my folders are all messed up. I rearranged it all on Itunes, synced again and that was a wasted hour! It went right back to the way just post upgrade.
So I did a restore to the morning before the update and its still not right. I can live with them not in folders, but a LOT are not showing on the phone, (though they do in Itunes). In Itunes they are scattered amongst 11 pages, but on the phone its mostly bare folders and only 3 pages.

A call to Apple had no help, other than to restore all the way to factory settings. Didn't help. The apps are still spread amongst 11 pages in Itunes,and when I try to sync, it seems to sync from the phone. Not from Itunes. The phone only shows about 4 pages. Sometimes it adds new apps from previous try. If I download them again it seems to stick. Some are paid for and Apps wants me to pay again.
still stuck. I see others have same issue and no one has responded to our issue.

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