if you restore from icloud you will lose all apps that have been pulled from the appstore for whatever reason. once an app has been pulled from apples app store for whatever reason (copyright infringement for one app i have) it is also gone from the icloud restore function, though i'm not sure what happens with its backed up data, i just know you can't restore the app. i think in that case you can later install from itunes, but it's a pain to have to remember all such apps and individually restore them.