Kryptonite comes in many colors.
In the comics Gold Kryptonite permanently removes Clark's powers.
In Smallville Blue Kryptonite temporarily removes Clark's powers while he remains in proximity.
Suppose the was a form of Kryptonite, call it prism K, that temporarily removes Clark's powers but only until his body could fully recharge, say in three to four years. Yes I said years.
So Trask finds this not Green K., he also finds blue K and Gold K. What he uses on Clark is his small supply of prism K, which in the aftermath is lost. Also lets say that exposure to this prism K renders Clark immune to Gold K but not Blue K.
Now it is a few years down the road and Nor and his minions invade and are defeated with Gold K.
