Hopefully, third time's the charm.
Goal Let $f\in L^{1}(\mathbb{R})$ be continuous function, such that
$\text{supp}(\hat{f})\subset [-1,1]$ and $f(n)\geq 0$ for all
$n\in\mathbb{Z}$. Then $$\int_{\mathbb{R}}f(y)dy\geq 0$$
Set $g(x):=\hat{f}(-x)=f^{\vee}(x)$. Clearly, $\text{supp}(g)\subset [-1,1]$, and since $g$ is continuous, $x^{n}g(x)\in L^{1}(\mathbb{R})$ for any $n\in\mathbb{N}$. By Fourier inversion and the hypothesis that $f$ is continuous, we see that $\hat{g}(\xi)=f(\xi)$ everywhere. Define a function $G:\mathbb{T}\rightarrow\mathbb{C}$ by
$$G(x)=\sum_{n\in\mathbb{Z}}g(x+n)=\sum_{n\in\mathbb{Z}}\hat{f}(-x-n)$$
I claim that the series defining $G$ converges uniformly and absolutely. Indeed, for any $x\in[0,1]$ and $n>2$, we have that $\left|x+n\right|>1$, whence $\hat{f}(-x-n)=0$. Since $\hat{f}$ is continuous, $G$ is the finite sum of continuous functions and therefore continuous.
I claim that $\hat{G}(m)=\hat{g}(m)=f(m)$ for all $m\in\mathbb{Z}$. Indeed, the second equality was established above, so it remains for us to prove the first.
$$\int_{0}^{1}G(x)e^{-2\pi i mx}dx=\sum_{n\in\mathbb{Z}}\int_{0}^{1}g(x+n)e^{-2\pi i m x}dx=\sum_{n\in\mathbb{Z}}\int_{n}^{n+1}g(x)e^{-2\pi i m(x-n)}dx=\int_{\mathbb{R}}g(x)e^{-2\pi i mx}dx$$
To complete the proof we need, we'll need a classical theorem of Fejer.
Theorem Denote the $N^{th}$ symmetric partial sum of the Fourier series of a
continuous function $h:\mathbb{T}\rightarrow\mathbb{C}$ by
$$S_{N}h(x)=\sum_{\left|m\right|\leq N}\hat{h}(m)e^{2\pi i m x}, x\in\mathbb{T}$$
and define the $N^{th}$ Cesaro mean of the partial
sums of the Fourier series of $h$ by
$$\sigma_{N}h(x)=\dfrac{1}{N}\sum_{j=0}^{N-1}S_{j}h(x), \ x\in\mathbb{T}$$
Then $\sigma_{N}h$ converges to $h$ uniformly on $\mathbb{T}$.
Using Fejer's theorem with $h=G$, we have in particular that $\sigma_{N}G(0)\rightarrow G(0)$. Since $S_{j}G(0)=\sum_{\left|m\right|\leq j}f(-m)=\sum_{\left|m\right|\leq j}f(m)$, it follows that $\sigma_{N}G(0)\geq 0$, whence
$$\int_{\mathbb{R}}f(y)dy=\hat{f}(0)=G(0)=\lim_{N\rightarrow\infty}\sigma_{N}G(0)\geq 0$$