Unroot, maybe factory reset and then update, root again?
or safe yourself the trouble and just flash the rom you want with Odin? In both cases you have to root again.
Samsung Galaxy S 4 I9505 | WanamLite v3.0
Samsung Galaxy S II I9100 : AOKP 4.2.1
HTC Touch Pro2 | ROM: Valkyrie 6.5.23115TR2.5
HTC HD2 | DarkStone1337 [FroyoStone Sense - V3.2]
HTC Desire : Oxygen v2.1.3