I thought at first you were asking how the characteristic function can be unique. There's no issue here, because e^ix is a well-defined function: for a given value of x, there is a unique value of e^ix. And so the expectation (an integral) has a unique value as well.
On second thought, it appears you're asking how it's possible, considering that e^ix is not injective (i.e., multiple x can have the same value of e^ix), that the original distribution can be completely recovered from the characteristic function. The answer to that is that you're probably missing the "t" in the expression: the characteristic function is a function of t, and although for a given value of t (e.g. t=1), the random variables $X$ and $X+2k\pi/t$ would have the same value of the characteristic function at that point, they would have different values at other t. So the characteristic functions are different, and yes, the distribution can be completely recovered from the characteristic function.