Another and more "modern" approach would be using the construction of the complete cotorsion pair ("a half of an abelian model structure") generated by a generating set of objects in a Grothendieck abelian category.
Let $F$ be a flat quasi-coherent sheaf that is a generator of $\operatorname{QCoh}(X)$, as in my previous answer. Consider the Grothendieck abelian category $\operatorname{Ch}(X)=\operatorname{Ch}(\operatorname{QCoh}(X))$ of complexes in $\operatorname{QCoh}(X)$. Denote by $S^\bullet$ the direct sum of all shifts of the one-term (stalk) complex $\dotsb\to0\to F\to0\to\dotsb$ and all shifts of the contractible two-term complex $\dotsb\to0\to F\overset{\mathrm{id}}\to F\to0\to\dotsb$. Then $S^\bullet$ is a $K$-flat complex and a generator of $\operatorname{Ch}(X)$.
Using the small object argument (see, e.g., the paper Eklof, Trlifaj "How to make Ext vanish"), one can construct for any complex $A^\bullet\in\operatorname{Ch}(X)$ a surjective morphism of complexes $G^\bullet\to A^\bullet$ with the following properties. The complex $G^\bullet$ is a transfinitely iterated extension of copies of the complex $S^\bullet$. The kernel $K^\bullet$ of the morphism of complexes $G^\bullet\to A^\bullet$ has the property that
$$
\operatorname{Ext}^1_{\operatorname{Ch}(X)}(S^\bullet,K^\bullet)=0.
$$
For any two complexes $C^\bullet$ and $D^\bullet$ in an abelian category $\mathsf{A}$, the group of all cochain homotopy classes of morphisms $C^\bullet\to D^\bullet[1]$ is naturally a subgroup of the group $\operatorname{Ext}^1_{\operatorname{Ch}(\mathsf A)}(C^\bullet,D^\bullet)$. Specifically, this is the subgroup formed by all the termwise (degreewise) split extensions.
In the situation at hand, it follows that all the maps of complexes $S^\bullet\to K^\bullet[-1]$ are homotopic to zero. Since $F$ is a generator of $\operatorname{QCoh}(X)$, one easily concludes that the complex $K^\bullet$ is acyclic. Thus $G^\bullet\to A^\bullet$ is a quasi-isomorphism.
On the other hand, the class of all $K$-flat complexes of flat quasi-coherent sheaves is closed under extensions and direct limits in $\operatorname{Ch}(X)$. Hence it is also closed under transfinitely iterated extensions. Therefore, the complex $G^\bullet$ is $K$-flat.
The small object argument is functorial. So one can produce the termwise surjective morphism of complexes $G^\bullet\to A^\bullet$ as above in such a way that it depends functorially on a complex $A^\bullet$.