seems to be no problem to change only the hole and via´s.
The button for changing parts is right under the- add parts button. A scroll down menu appears and than you choose package from it. With the next click on layout symbol you can change to whatever you want.
if you change a package which is already used and you add the changed package to the board, eagle recognice that you have a new package and is updating the board, very handy.
If you just need the package once i would definetly build a new package with copy and paste.