For the sake of trying to offer some sort of answer based off of Tim's first comment:
Let $\mathcal{E}$ be a coherent sheaf on $M$ and $(((E_i, \nabla_i)\to U_i \subset M_i)_{i \in I}$ be a local resolution of $\mathcal{E}$ subordinate to cover $\mathcal{U}= \{U_i\}_I$ with chosen connections and $g_{\bullet}$ a twisting cochain a la O'Brian, Toledo. and Tong. Define for each $(\alpha_0, \ldots, \alpha_p)$ the element $c^p_{(\alpha_0, \ldots, \alpha_p)}:= (\nabla g)^p_{(\alpha_0, \ldots, \alpha_p)} \in \check{C}^p(\mathcal{U}, \Omega_{hol}^p(\mathcal{U}, Hom^{\bullet}(E_{\alpha_p}, E_{\alpha_0})))$.
The collection of such elements for each $p$, $c^p_{\bullet}$ is Čech-Hom closed (I think this goes back to Atiyah, but we spelled out the details in GMTZ Prop 3.11) and we can put the zero differential on $\Omega^{\bullet}$ so that these elements arrange to form classes in a bicomplex. Alternatively, you can strip the hom-differential portion of the Čech complex out and say that these elements have components in a different bicomplex $c^p = \sum_{q = 0}^{\infty}c^{p,q}\in \check{C}^p(\mathcal{U}, \Omega_{hol}^p(\mathcal{U}, Hom^{q}(E_{\alpha_p}, E_{\alpha_0})))$.
Now since equivalent coherent sheaves induce cohomologous characteristic classes ``$tr_g(c^{\bullet})$'', we hopefully can rework those statements to obtain invariants in (at worst) this Čech-Hom space or maybe (at best) Čech-Forms space so that
- Equivalent coherent sheaves induces cohomologous classes, and
- A vector bundle thought of as a coherent sheaf has $c^{p,q}=0$ for $q< 0$.