If they have re-appeared on your phone, if you press and hold the individual app it will start to shake and then you can select to remove it. This will not remove it or the data from your computer, but just your phone.
You can update via itunes which apps you would like individually on your phone and on your ipad.
itunes seems to update quite a lot and the layout may have changed, so it's hard to explain exactly where to go to do this, but there should be some clear menus when you plug in your device.
Hope this helps!
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