I think it should work as follows. One of the key ideas is that it necessarily involves carefully considering the geometry of affine schemes.
If $V \to U \to X$ are open subfunctors, then take a map $h_A \to X$ for some ring $A$. The pullback $U_A = h_A \times_X U \to h_A$ can be assumed to be the map $h_{A,I} \to h_A$ for an ideal $I$ in $A$, where $$h_{A,I}(R) = \{\phi: A \to R : \phi(I)R = R\}.$$ We have a commutative diagram
$$
\require{AMScd}\begin{CD}
h_{A,I} @>>> U \\
@VVV @VVV \\
h_A @>>> X
\end{CD}$$
Now, motivated by the fact that $D(I)$ is covered by the collection $\{D(f)\}_{f \in I}$, we will consider the affine schemes $h_{A,(f)} \cong h_{A_f}$ (localization at the element $f \in I$).
There is a natural inclusion $h_{A_f} \to h_{A,I}$ for all $f \in I$, given by the fact that if $\phi(f)R = R$, then $\phi(I)R = R$. So we can consider the diagram
$$
\require{AMScd}\begin{CD}
h_{A,J_f} @>>> h_{A,I} \times_U V @>>> V \\
@VVV @VVV @VVV \\
h_{A_f} @>>> h_{A,I} @>>> U \\
@. @VVV @VVV \\
@. h_A @>>> X
\end{CD}$$
where the $J_f$ come from the fact that $V \to U$ is an open subfunctor using the map $h_{A_f} \to h_{A,I} \to U$, then pulling back the resulting ideal in $A_f$ to $A$. This tells us that for any morphism $\phi: A \to R$, we have $$\phi(J_f)R = R \Longleftrightarrow \phi(f)R = R, X(\phi)(u) \in V(R)$$ where $u$ is the universal element in $X(A)$ for the morphism $h_A \to X$.
Now note that $$(h_{A,I} \times_U V)(R) = \{\phi: A \to R : \phi(I)R = R, X(\phi)(u) \in V(R)\}.$$ Note further that $$h_{A,J_i}(R) = \{\phi: A \to R : \phi(f)R = R, X(\phi)(u) \in V(R)\}.$$
Define $J = \bigcup J_i$ (sum of ideals). Then I think you want to show that $h_{A,I} \times_U V \cong h_{A,J}$, which will finish the proof. This is the same as showing that $$\phi(J)R = R \Longleftrightarrow \phi(I)R = R, X(\phi)(u) \in V(R).$$ To do this, you first show that it's true when $R=K$ is a field: this is essentially because $\phi(I)K = K$ is the same as $\phi(I) \neq 0$, and the fact that $h_{A,I} \times_U V$ is covered by the $h_{A,J_f}$, which follows from the fact that $\{h_{A_f}\}$ covers $h_{A,I}$ (in the sense of Demazure and Gabriel, which can be verified directly) Check this.
So $(h_{A,I} \times_U V)|_{Fields} \cong h_{A,J}|_{Fields}$. Demazure and Gabriel prove in Prop. 4.12 in their first section of the first chapter that open subfunctors of a functor $F$ are in bijection with open subsets of $|F|$. Since the underlying set of the geometric realization only depends on the restriction of $F$ to fields, and since $h_{A,J} \to h_A$ is an open subfunctor, we see that the underlying set of $|h_{A,I} \times_U V|$ is open in $|h_A| (=Spec(A))$ (in fact it's $D(J)$). But then, you can use Prop 4.12 in I,i in Demazure and Gabriel's book (English version), which shows that there's a bijection between the open subfunctors of a functor $F$ and the open subsets of $|F|$, which forces the isomorphism.
You can check that the proof of this proposition doesn't assume the result you want to show.