Index type invariants for twisted signature complexes and homotopy invariance

For a closed, oriented, odd dimensional manifold $X$, we define the rho invariant $\rho(X,E,H)$ for the twisted odd signature operator valued in a flat hermitian vector bundle $E$, where $H = \sum i^{j+1} H_{2j+1}$ is an odd-degree closed differential form on $X$ and $H_{2j+1}$ is a real-valued differential form of degree ${2j+1}$. We show that the twisted rho invariant $\rho(X,E,H)$ is independent of the choice of metrics on $X$ and $E$ and of the representative $H$ in the cohomology class $[H]$. We establish some basic functorial properties of the twisted rho invariant. We express the twisted eta invariant in terms of spectral flow and the usual eta invariant. In particular, we get a simple expression for it on closed oriented 3-dimensional manifolds with a degree three flux form. A core technique used is our analogue of the Atiyah-Patodi-Singer theorem, which we establish for the twisted signature operator on a compact, oriented manifold with boundary. The homotopy invariance of the rho invariant $\rho(X,E,H)$ is more delicate to establish, and is settled under further hypotheses on the fundamental group of $X$.