iTunes mess after iPad swap

Swaped my 1 against my spouse's 2 recently.
Backed them up before, and then restored the 1s backup to the 2 and vice versa the 2s backup to the 1.
Now when I sync in iTunes, I see the Apps I actually have on my 2 initially, but as I start the synching process, there's suddenly much more Apps displayed, and also the memory indication changes.
It also seems that new installed apps are not listed in iTunes after sync.

What a mess, although I researched the swap carefully before...

Any hints how to solve this?
Thanks!

or better asked

is there a way to completely delete all stored settings from iTunes and set it up fresh from my IPad 2 again?