Here is an attempt to make levap's idea seem more natural:
We start with the following basic observation:
If $\Phi:(E,\nabla^E,\eta_E) \to (F,\nabla^F,\eta_F)$ is an isometric bundle morphism which respects the connections, then
$\delta^F (\Phi_*\alpha) =\Phi_* (\delta^E (\alpha))$ for every $\alpha
\in \omega^k(M,E)$.
($\Phi_*: \omega^k(M,E) \to \omega^k(M,F)$ is the induced morphism which is the action of $\Phi$ on the values of the forms).
Define $\Phi:E \to E$ via $\langle \Phi(v),u \rangle_2=\langle v,u \rangle_1$.
Consider $\Phi$ as a map $(E,\eta_2) \to (E,\eta_2)$.
$\Phi$ is self-adjoint:
$$ \langle \Phi(v),u \rangle_2=\langle v,u \rangle_1=\langle u,v \rangle_1=\langle \Phi(u),v \rangle_2=\langle v,\Phi(u) \rangle_2$$
$\Phi$ is positive:
$$\langle \Phi(v),v \rangle_2=\langle v,v \rangle_1$$
Thus, there is a unique self-adjoint positive square root $ \sqrt \Phi: (E,\eta_2) \to (E,\eta_2)$ map, which is easily seen to be an isometry when considered as a map $(E,\eta_1) \to (E,\eta_2)$:
$$ \langle \sqrt \Phi(v),\sqrt \Phi(u) \rangle_2=\langle v,\Phi(u) \rangle_2=\langle v,u \rangle_1$$
We claim $\sqrt \Phi$ is $\nabla$-parallel:
levap showed in his answer that $\nabla_x \Phi=0$. Thus, by a Leibnitz property it follows that:
$$0=\nabla_x \Phi=\nabla_x (\sqrt \Phi)^2= (\nabla_x \sqrt \Phi) \sqrt \Phi + \sqrt \Phi (\nabla_x \sqrt \Phi)$$
This is a Sylvester equation, hence there is a unique solution $\nabla_x \sqrt \Phi=0$.
This implies that $\sqrt \Phi:(E,\nabla,\eta_1) \to (E,\nabla,\eta_2)$ preserves all the structures, thus by the observation above:
$$ \delta^2 (\sqrt \Phi_*\alpha) =(\sqrt \Phi)_* (\delta^1 (\alpha)) $$
Replacing $\alpha$ with $\sqrt \Phi_*\alpha$, we obtain
$$ \delta^2 (\Phi_*\alpha) =(\sqrt \Phi)_* (\delta^1 (\sqrt \Phi_* \alpha)),$$ so
$$ \delta^2 (\Phi_*\alpha) = \delta^1 (\Phi_*\alpha) \iff \delta^1 (\Phi_*\alpha) =(\sqrt \Phi)_* (\delta^1 (\sqrt \Phi_* \alpha)),$$ that is if and only if $\delta^1$ commutes with $\sqrt \Phi_*$.
However, it is not clear how to show this...
Edit:
I had the following conjecture:
Let $(E,\nabla^E), (F,\nabla^F)$ be smooth vector bundles over $M$ (with connections).
Let $ \Phi:E \to F$ be a bundle isomorphism which maps $\nabla^E$-compatible metrics to $\nabla^F$-compatible metrics. Then
$\delta^F (\Phi_*\alpha) =\Phi_* (\delta^E (\alpha))$ for every $\alpha
\in \omega^k(M,E)$,
where $\delta^E$ is the corresponding adjoint to $d_{\nabla^E}$ taken w.r.t any $\nabla^E$-compatible metric, and $\delta^F$ is the corresponding adjoint to $d_{\nabla^F}$ taken w.r.t the any $\nabla^F$-compatible metric.
A special case of this conjecture, for $E=F,\Phi=\operatorname{Id}$ is exactly the claim that the adjoint does not depend on the $\nabla^E$-compatible metric chosen.
However, this conjecture is clearly false in general, since there are connections $\nabla^E$ with no $\nabla^E$-compatible metrics, so every bundle isomorphism $\Phi:E \to F$ satisfies the requirement vacuously, but there is no reason for it to commute with $\delta$.
What is true is the following statement:
Let $ \Phi:E \to F$ be a parallel bundle isomorphism (i.e $\nabla \Phi=0$), then $\Phi$ commutes with $\delta$'s taken w.r.t $\nabla^E,\nabla^F$ compatible metrics. Indeed, given $\nabla^E$-compatible metric, $\Phi:(E,\nabla^E,\eta_E) \to (F,\nabla^F,\Phi_*\eta_E)$ preserve all the structures, hence commute with $\delta$.