The setup isn't important, but in case you're curious, this is a physically relevant thing I'm trying to calculate that should have a finite value. This equation gives the electric field of a small patch of voltage $V$ of length $l$ on the surface of a grounded conducting cylinder of radius $R$ in the center of the cylinder: $$ |\mathbf{E}|=\frac{Vl^2}{2\pi R^3}\lim_{\epsilon\rightarrow 0^+}\sum_{m=1}^\infty \frac{\alpha_{1m}\exp\left(-\alpha_{1m}\epsilon\right)}{J_2(\alpha_{1m})}\approx 1.77578 \frac{Vl^2}{2\pi R^3} $$ $J_1$ is the first Bessel function of the first kind, and $\alpha_{1m}$ is it's $m$'th zero (not including the one at $x=0$). The $\approx$ comes from me evaluating this numerically. I understand that I cannot move the limit into the sum because if I do, the sum no longer converges. What I don't understand is why it even has a well defined limit with the limit outside of the sum.
For large $m$, the zeros go toward $\alpha_{1m}\rightarrow (m+1/4)\pi$. For large inputs $J_2(x)$ asymptotes to: $$ J_2(x)\rightarrow -\sqrt{\frac{2}{\pi}}\sin\left(x+\frac{\pi}{4}\right)\sqrt\frac{1}{x} $$ So it seems to me that the sum for large $m$ turns into: $$ \sum_{m=N}^\infty m^{3/2} (-1)^m\exp(-m\pi\epsilon) $$ And even if I add even and odd terms together, I should get $$ \sum_{m'=N/2}^\infty m'^{1/2} \exp(-2m'\pi\epsilon) $$ So I think as $\epsilon$ goes to zero, my sum will go to infinity. Certainly the above sum diverges, so I must have done something too handwavy with limits here. Strangely though, as $\epsilon$ goes to zero, the sum goes to a finite value.
New Answer. In this answer, we derive an integral representation of the limit. Using the special case of DLMF 10.6.2,
$$ J_1'(z) = -J_2(z) + \frac{J_1(z)}{z}, $$
we may write the sum as
\begin{align*} \sum_{m=1}^{\infty} \frac{\alpha_{1,m}e^{-\epsilon \alpha_{1,m}}}{J_2(\alpha_{1,m})} &= -\sum_{m=1}^{\infty} \frac{\alpha_{1,m}e^{-\epsilon \alpha_{1,m}}}{J_1'(\alpha_{1,m})} = - \frac{1}{2\pi i} \int_{\mathcal{C}} \frac{z e^{-\epsilon z}}{J_1(z)} \, \mathrm{d}z. \end{align*}
Here, $\mathcal{C}$ denotes the Hankel contor traversed in the positive sense. Now by noting that $J_1(z)$ grows exponentially as $\operatorname{Im}(z) \to \pm\infty$ in the region $\left|\arg(z)\right| \leq \frac{\pi}{2}$, we can deform the contour $\mathcal{C}$ to the imaginary axis traversed from top to bottom. Hence,
\begin{align*} \sum_{m=1}^{\infty} \frac{\alpha_{1,m}e^{-\epsilon \alpha_{1,m}}}{J_2(\alpha_{1,m})} &= - \frac{1}{2\pi i} \int_{i\infty}^{-i\infty} \frac{z e^{-\epsilon z}}{J_1(z)} \, \mathrm{d}z \\ &= \frac{1}{2\pi} \int_{-\infty}^{\infty} \frac{xe^{-i\epsilon x}}{I_1(x)} \, \mathrm{d}x \\ &\to \bbox[color:blue; padding:8px; border:1px dotted navy;]{ \frac{1}{2\pi} \int_{-\infty}^{\infty} \frac{x}{I_1(x)} \, \mathrm{d}x } \quad \text{as $\epsilon \to 0^+$}, \end{align*}
where we substituted $z = ix$ in the second step and $I_1(z)$ is the modified Bessel function of the first kind and order $1$. Thanks to the exponential growth of $I_1(x)$ as $x \to \pm\infty$, this integral can be efficiently approximated, yielding the numerical value of
$$ \approx 1.7757859970218740923 $$
as observed by OP.
Old Answer. In fact, turns out that
$$ \lim_{\varepsilon \to 0^+} \sum_{n=1}^{\infty} \frac{(-1)^n}{n^s} e^{-\varepsilon n} = -(1 - 2^{1-s}) \zeta(s) \tag{1} $$
for any $s \in \mathbb{C}$. In particular, when $s = -\frac{3}{2}$, we get
$$ \lim_{\varepsilon \to 0^+} \sum_{n=1}^{\infty} (-1)^n n^{3/2} e^{-\varepsilon n} = -(1 - 2^{5/2}) \zeta(-3/2) \approx -0.118681. $$
Although I am no expert of Bessel functions, I guess an analogous behavior is occurring in OP's sum limit as well.
Finally, let me demonstrate why we expect the limit in $\text{(1)}$ to have a finite value. To this end, let us consider, for example, the sum $ \sum_{n=1}^{\infty} (-1)^n n^2 $. Although this does not converge,
$$ \sum_{n=1}^{\infty} (-1)^n n^2 e^{-\varepsilon n} = - \frac{(1 - e^{-\varepsilon})e^{-\varepsilon}}{(1+e^{-\varepsilon})^3}, \qquad \operatorname{Re}(\varepsilon) > 0 $$
and hence letting $\varepsilon \to 0^+$ makes this converge to a finite value, which is $0$ in this case. This shows that this "exponential regularization" (or more commonly, Abel summation) is capable of facilitating cancellations between $(-1)^n n^2$'s. A similar thing occurs when $n^2$ is replaced by any power of $n$.