[guided]We need to compare the entropy of the averaged slice $H$ with the average of the entropies of the unaveraged slices $h(\cdot,z)$. A direct convexity argument for $g\mapsto \operatorname{Ent}_{\mu_k}(g)$ is delicate because entropy contains a negative term involving the mean. The clean scalar way to handle this is to rewrite entropy as a relative entropy integrand.
Fix $k\in\{1,\dots,n\}$ and fix $x_{\leq k-1}=(x_1,\dots,x_{k-1})\in E_{\leq k-1}$ outside the null set where the relevant sections are measurable and integrable. Define the measurable map $h:E_k\times E_{>k}\to[0,\infty)$ by
\begin{align*}
h(y,z) := f(x_1,\dots,x_{k-1},y,z_{k+1},\dots,z_n).
\end{align*}
Define the average over the later variables as the measurable map $H:E_k\to[0,\infty)$ with
\begin{align*}
H(y) := \int_{E_{>k}} h(y,z)\,d\mu_{>k}(z).
\end{align*}
Then $H(y)=F_k(x_1,\dots,x_{k-1},y)$ for $\mu_k$-almost every $y$.
Now define the scalar function $\Psi:[0,\infty)\times[0,\infty)\to[-e^{-1},\infty]$ by $\Psi(u,v)=u\log(u/v)$ for $u>0$ and $v>0$, by $\Psi(0,v)=0$ for $v\geq0$, and by $\Psi(u,0)=+\infty$ for $u>0$. This function is the perspective of the convex function $\Phi(t)=t\log t$, so $\Psi$ is jointly convex in the two scalar variables. This joint convexity is the correct replacement for the invalid subtraction of two convexity inequalities. We will also need a lower bound: for $v>0$, writing $r=u/v$ gives $\Psi(u,v)=v r\log r$, and $r\log r\geq -e^{-1}$ for $r\geq0$. Thus $\Psi(u,v)\geq -v/e$, and the same lower bound holds under the stated conventions when $v=0$.
For each later-coordinate value $z\in E_{>k}$ whose section is integrable, define its $E_k$-mean as the map $m:E_{>k}\to[0,\infty]$ by
\begin{align*}
m(z) := \int_{E_k} h(y,z)\,d\mu_k(y).
\end{align*}
Define the mean of $H$ by
\begin{align*}
M := \int_{E_k} H(y)\,d\mu_k(y).
\end{align*}
[Fubini's theorem](/theorems/2961) applies to the non-negative integrable function $h$, so the two ways of computing the total mean agree:
\begin{align*}
M = \int_{E_{>k}} m(z)\,d\mu_{>k}(z).
\end{align*}
The entropy of $H$ can now be written as
\begin{align*}
\operatorname{Ent}_{\mu_k}(H) = \int_{E_k}\Psi(H(y),M)\,d\mu_k(y).
\end{align*}
For fixed $y\in E_k$, the pair $(H(y),M)$ is the $\mu_{>k}$-average of the pairs $(h(y,z),m(z))$. Therefore [Jensen's Inequality](/theorems/9) for the jointly convex scalar function $\Psi$ gives
\begin{align*}
\Psi(H(y),M) \leq \int_{E_{>k}}\Psi(h(y,z),m(z))\,d\mu_{>k}(z).
\end{align*}
Integrating this inequality over $E_k$ requires a signed-integral justification, because $\Psi$ is not non-negative. The lower bound gives
\begin{align*}
\Psi(H(y),M)^- \leq M/e
\end{align*}
for $\mu_k$-almost every $y$, and
\begin{align*}
\Psi(h(y,z),m(z))^- \leq m(z)/e
\end{align*}
for $\mu_k\otimes\mu_{>k}$-almost every $(y,z)$. Since Fubini gave
\begin{align*}
\int_{E_{>k}}m(z)\,d\mu_{>k}(z)=M<\infty,
\end{align*}
these negative parts are integrable. We may therefore apply [Fubini's theorem](/theorems/2961) to the negative parts and Tonelli's theorem to the positive parts, obtaining
\begin{align*}
\operatorname{Ent}_{\mu_k}(H) \leq \int_{E_{>k}}\int_{E_k}\Psi(h(y,z),m(z))\,d\mu_k(y)\,d\mu_{>k}(z).
\end{align*}
For fixed $z$, the inner integral is exactly the entropy of the slice $h(\cdot,z)$ with respect to $\mu_k$:
\begin{align*}
\int_{E_k}\Psi(h(y,z),m(z))\,d\mu_k(y)=\operatorname{Ent}_{\mu_k}(h(\cdot,z)).
\end{align*}
Thus
\begin{align*}
\operatorname{Ent}_{\mu_k}\bigl(F_k(x_1,\dots,x_{k-1},\cdot)\bigr) \leq \int_{E_{>k}}\operatorname{Ent}_{\mu_k,k}(f)(x_1,\dots,x_{k-1},z_{k+1},\dots,z_n)\,d\mu_{>k}(z),
\end{align*}
with the right-hand side interpreted in the extended sense for exceptional slices.[/guided]