Here, I answer the OP's question directly. While Poisson's summation formula yields the correct result, it does not seem to provide a rigorous derivation.
Poisson's summation formula:
\begin{align*}
\sum_{n=-\infty}^\infty F(n+t) & = \sum_{m=-\infty}^\infty \tilde{F} (2 \pi m) e^{2 \pi i m t}
\end{align*}
where
\begin{align*}
\tilde{F} (y) = \int_{-\infty}^\infty F(s) e^{-i y s} ds
\end{align*}
So
\begin{align*}
F (s) = \frac{e^{2 \pi i \alpha s}}{x^2-s^2}
\end{align*}
and
\begin{align*}
\tilde{F} (y) = \int_{-\infty}^\infty \frac{e^{2 \pi i \alpha s - iy s}}{x^2-s^2} ds \qquad (1)
\end{align*}
We have the Fourier transform:
\begin{align*}
\int_{-\infty}^\infty \frac{e^{-i ys}}{x^2-s^2} ds & = \frac{\pi}{x} \sin (xy) sgn (y)
\end{align*}
Using this in (1):
\begin{align*}
\tilde{F} (y) = \frac{\pi}{x} \sin (x (2 \pi \alpha - y)) sgn (2 \pi \alpha - y)
\end{align*}
and putting $y=2 \pi m$:
\begin{align*}
\tilde{F} (2 \pi m) = \frac{\pi}{x} \sin (x 2 \pi (\alpha - m)) sgn (2 \pi (\alpha - m))
\end{align*}
then
\begin{align*}
\sum_{n=-\infty}^\infty F(n+t) & =\sum_{m=-\infty}^\infty \tilde{F} (2 \pi m) e^{2 \pi i m t}
\nonumber \\
& = \frac{\pi}{x} \sum_{m=-\infty}^\infty \sin (x 2 \pi (\alpha - m)) sgn (2 \pi (\alpha - m)) e^{2 \pi i m t}
\nonumber \\
& = \frac{\pi}{x} \sum_{m=-\infty}^\infty \sin (x 2 \pi (\alpha + m)) sgn (2 \pi (\alpha + m)) e^{-2 \pi i m t}
\end{align*}
Presence of sgn:
Put $\alpha = r + \{ \alpha \}$ where $\{ \alpha \}$ is the fractional part of $\alpha$, then
\begin{align*}
\sum_{n=-\infty}^\infty F(n+t) & = \frac{\pi}{x} \sum_{m=-\infty}^\infty \sin (2 \pi x (r+m + \{ \alpha \})) sgn (2 \pi (r+m + \{ \alpha \})) e^{-2 \pi i m t}
\nonumber \\
& = \frac{\pi}{x} e^{2 \pi i t r} \sum_{m=-\infty}^\infty \sin (2 \pi x (r+m + \{ \alpha \})) sgn (2 \pi (r+m + \{ \alpha \})) e^{-2 \pi i (m+r) t}
\nonumber \\
& = \frac{\pi}{x} e^{2 \pi i t r} \sum_{m=-\infty}^\infty \sin (2 \pi x (m + \{ \alpha \})) sgn (2 \pi (m + \{ \alpha \})) e^{-2 \pi i m t}
\nonumber \\
& = \frac{\pi}{x} e^{2 \pi i t r} [- \sum_{m=-\infty}^{-1} \sin (2 \pi x (m + \{ \alpha \})) e^{-2 \pi i m t} + \sum_{m=0}^\infty \sin (2 \pi x (m + \{ \alpha \})) e^{-2 \pi i m t}]
\end{align*}
Summing geometric series and taking imaginary part:
Then $t=0$,
\begin{align*}
\sum_{n=-\infty}^\infty \frac{e^{2 \pi i \alpha n}}{x^2-n^2} & = \frac{\pi}{x} [- \sum_{m=-\infty}^{-1} \sin (2 \pi x (m+\{ \alpha \})) + \sum_{m=0}^\infty \sin (2 \pi x (m + \{ \alpha \}))]
\nonumber \\
& = \frac{\pi}{x} [\sum_{m=1}^\infty \sin (2 \pi x (m-\{ \alpha \})) + \sum_{m=0}^\infty \sin (2 \pi x (m + \{ \alpha \}))]
\nonumber \\
& = \frac{\pi}{x} Im [\sum_{m=1}^\infty e^{i2 \pi x (m-\{ \alpha \})} + \sum_{m=0}^\infty e^{i2 \pi x (m + \{ \alpha \})})]
\nonumber \\
& = \frac{\pi}{x} Im [ \frac{e^{-i2 \pi x \{ \alpha \}}}{e^{- i2 \pi x} - 1} + \frac{e^{i2 \pi x \{ \alpha \}}}{1-e^{i2 \pi x}}]
\nonumber \\
& = \frac{\pi}{x} Im [-\frac{e^{-i2 \pi x \{ \alpha \} +i \pi x}}{e^{i \pi x} - e^{-i \pi x}} - \frac{e^{i2 \pi x \{ \alpha \} - i \pi x}}{e^{i \pi x} - e^{-i \pi x}}]
\nonumber \\
& = \frac{\pi}{x} Im [\frac{i}{2} \frac{e^{-i2 \pi x \{ \alpha \} +i \pi x}}{\sin (\pi x)} + \frac{i}{2} \frac{e^{i2 \pi x \{ \alpha \} - i \pi x}}{\sin (\pi x)}]
\nonumber \\
& = \frac{\pi}{x} \frac{\cos (\pi x (2\{ \alpha \} - 1))}{\sin (\pi x)}
\end{align*}
giving the correct answer.
How to make it legitimate?
Doing $\sum_{n=0}^\infty e^{2 \pi i xm} = \frac{1}{1-e^{2 \pi i x}}$ is not legitimate as this
\begin{align*}
(1 - e^{2 \pi i x}) \sum_{n=0}^N e^{2 \pi i xm} = 1 - e^{2\pi i (N+1)x} = 1 - \cos (2 \pi (N+1)x) - i \sin (2 \pi (N+1)x)
\end{align*}
is ill-defined in the limit $N \rightarrow \infty$.
How do you adjust the above calculation to make it legitimate?