Consider the following differential equations $$ \begin{cases} \partial_t X(t) = -i \alpha X(t) + \beta Y(t), \\ \partial_t Y(t) = -i \alpha Y(t) - \beta X(t). \end{cases}\label{1}\tag{1} $$ with $\alpha$, $\beta$ some complex constants (independent of $t$).
Case-1 [Time domain]: The solution (with initial condition, say $X(0) = 1, Y(0) = 0$) reads $$ \begin{cases} X(t) = \frac{1}{2}[e^{-ist} + e^{-idt}], \\ Y(t) = -\frac{1}{2} [e^{-ist} - e^{-id t}], \end{cases}\label{2}\tag{2} $$ where $s = \alpha + \beta$ and $d = \alpha - \beta$. Now, the Fourier transform $$ \mathscr{F}[A(t)] = A(\omega) = \int_{-\infty}^{\infty} dt e^{i\omega t} A(t) $$ of \eqref{2} reads: $$ \begin{cases} X(\omega) = \frac{1}{2}[ \delta (\omega - s) + \delta (\omega + s)], \\ Y(\omega) = -\frac{i}{2}[ \delta (\omega - s) - \delta (\omega + s)] \end{cases}\label{3}\tag{3} $$ Case-2 [Fourier domain]: Taking Fourier transform of \eqref{1}, we have $$ \begin{cases} -i \omega X(\omega) = -i \alpha X(\omega) + \beta Y(\omega),\\ -i\omega Y(\omega) = -i\alpha Y(\omega) - \beta X(\omega). \end{cases}\label{4}\tag{4} $$ The solution of \eqref{4} (using Mathematica) turns out to be $$ \begin{cases} X(\omega) = 0, \\ Y(\omega) = 0. \end{cases}\label{5}\tag{5} $$ Clearly solution \eqref{5} is not the same as solution \eqref{3}. Am I missing too many things here?
Edit: My question is simple. How to start with equation \eqref{4} and obtain equation \eqref{3}?