[guided]This is the only place where the Skolem functions are used. Let
\begin{align*}
\psi(z_1,\dots,z_m)
\end{align*}
be the formula
\begin{align*}
\exists x\,\varphi(x,z_1,\dots,z_m),
\end{align*}
and assume, as the induction hypothesis, that $\varphi$ already has the same truth value in $N$ and in $M$ for all parameter tuples from $H$. Fix a tuple $a=(a_1,\dots,a_m)\in H^m$.
We first prove the direction from $M$ to $N$. Suppose
\begin{align*}
M \models \exists x\,\varphi(x,a).
\end{align*}
The problem is that an arbitrary witness in $M$ need not lie in $H$, so it need not be available as an element of $N$. The chosen Skolem function supplies a controlled witness. By hypothesis, the function
\begin{align*}
s_\varphi: |M|^m &\to |M|
\end{align*}
satisfies
\begin{align*}
M \models \varphi(s_\varphi(a),a)
\end{align*}
whenever $M \models \exists x\,\varphi(x,a)$. Because $a\in H^m$ and $H$ is closed under this Skolem function, we also have
\begin{align*}
s_\varphi(a)\in H.
\end{align*}
Now the induction hypothesis applies to the tuple $(s_\varphi(a),a)\in H^{m+1}$ and gives
\begin{align*}
N \models \varphi(s_\varphi(a),a).
\end{align*}
Therefore $N$ has a witness to the existential formula, namely $s_\varphi(a)$, and hence
\begin{align*}
N \models \exists x\,\varphi(x,a).
\end{align*}
For the reverse direction, suppose
\begin{align*}
N \models \exists x\,\varphi(x,a).
\end{align*}
Then there exists an element $b\in H$ such that
\begin{align*}
N \models \varphi(b,a).
\end{align*}
Here no Skolem function is needed: every element of $N$ is already an element of $M$, because the universe of $N$ is $H\subseteq |M|$. Since $(b,a)\in H^{m+1}$, the induction hypothesis gives
\begin{align*}
M \models \varphi(b,a).
\end{align*}
Thus $b$ is also a witness in $M$, so
\begin{align*}
M \models \exists x\,\varphi(x,a).
\end{align*}
Both directions are proved, so existential formulas agree.[/guided]