Now a complete proof, using some of the suggestions in the previous version of this answer.
Note that \begin{equation} G:= F_n''(x) x^{2-2 n} \left(x^{2 n}+1\right)^2 \left(x^{4 n}+x\right)^2 \left(x^{2 n+1}-1\right)^2 \left(x^{2 n+1}+1\right)^2 \left(x^{2 n+2}-1\right)^2 \end{equation} is a polynomial in $n$, $x$, and $y:=x^{2n}$, of degree $2$ in $n$: \begin{equation} G=a+bn+cn^2, \end{equation} where $a,b,c$ are certain polynomials in $x,y$.
The check of $G\ge0$ for $n=2,\dots,11$ is straightforward. So, assume $n\ge12$, whence $0<y<x^{24}<x^{12}$. We also always assume that $0<x<1$, $0<y<x^{12}$ , \begin{equation} n=\frac{\ln y}{2\ln x}; \tag{1} \end{equation} the latter relation is of course just another form of the equality $y=x^{2n}$.
Note that \begin{equation} a\ge0 \end{equation} for all $x,y$ in $(0,1)$. This is is easily verified by using Tarski's theory on quantifier elimination. In Mathematica, this theory is implemented via command Reduce[] and related commands. One can also use resultants or other tools to the same end. Details of the calculations can be seen in the Mathematica notebook and its pdf image .
Next, introduce \begin{equation} y_0 := 164/10^5, \quad y_1 := 695/1000,\quad x_* := 869/1000. \end{equation}
The following cases are exhaustive:
Case 1: $y\le y_1$. Then a Reduce[] quickly shows that $c\ge0$. So, for the derivative $G'_n$ of $G$ in $n$, we have $$G'_n=b+2cn\ge b+24c.$$ Now we have to distinguish two subcases:
Subcase 1.1: $y\le y_1$ and ($y\ge y_0$ or $x\le x_*$). Then, using another two instances of Reduce[], with conditions $y\ge y_0$ and $x\le x_*$ respectively, we get $b + 24 c \ge 0$, so that $G'_n\ge0$, so that $G$ is increasing in $n\ge12$, and so, $G\ge G|_{n=12}$, which latter is $\ge0$, by yet another two instances of Reduce[], with conditions $y\ge y_0$ and $x\le x_*$ respectively. So, $G\ge0$ in Subcase 1.2.
Subcase 1.2: $y\le y_1$ and $y<y_0$ and $x>x_*$. Then, of course, the condition $y\le y_1$ is redundant. Let here \begin{equation} \rho(x):=\frac7{2(1-x)}. \end{equation} Another Reduce[] quickly shows that $b+c\rho(x)\ge0$. So, similarly to Subcase 1.1, for all $n\ge\rho(x)/2$ we get $G\ge G|_{n=\rho(x)/2}$, which latter is $\ge0$, by another Reduce[]. In this subcase, it remains to note that for our particular $n$, as in $(1)$, we indeed have $n\ge\rho(x)/2$. This follows because for $y<y_0$ and $x>x_*$ \begin{equation} \ln\frac1y>\ln\frac1{y_0}>1.08\frac7{2(1-x_*)}\,\ln\frac1{x_*} >\frac7{2(1-x)}\,\ln\frac1{x}=\rho(x)\ln\frac1{x}. \end{equation} So, $G\ge0$ in Subcase 1.2 as well.
It remains to consider
Case 2: $y\le y_1$. Then another Reduce[] yields $b\ge0$. So, if $c\ge0$, then trivially $G\ge0$ (since $a\ge0$ always). So, without loss of generality, $c<0$ and hence $G$ is concave in $n$. So, it is enough to bracket the $n$ as in $(1)$ between some simple rational expressions $n_1$ and $n_2$ such that $G|_{n=n_1}\ge0$ and $G|_{n=n_2}\ge0$.
In Case 2, $y$ is "close" to $1$ and hence, in view of inequality $y<x^{24}$, so is $x$: $x>y_1^{1/12}>0.97$. So, it is a bit more convenient here to change variables $x, y$ to "small variables" $u:=1-x$ and $v:=1-y$. Then $0<v<1-y_0=0.305$ and $1-u=x>y^{1/12}=(1-v)^{1/12}>1-v/3$, whence $u<v/3$. Let now $t:=u/v$, so that $0<t<1/3$.
The mentioned brackets $n_1$ and $n_2$ are respectively $\ell_1/2$ and $\ell_2/2$, where
\begin{equation}
\ell_1:=\frac1t,\quad\ell_2:=\frac{(2 - v) (1 - t v)}{t (1 - v) (2 - t v)}.
\end{equation}
It is not hard to see (details on this are in the same Mathematica notebook) that then indeed $n_1 < n < n_2$.
Finally, another two instances of Reduce[] show that indeed $G|_{n=n_1}\ge0$ and $G|_{n=n_2}\ge0$.
The proof is complete.