In this paper, we consider the effects of nonlinear phase modulation on frequency conversion by four-wave mixing (Bragg scattering) in the low-conversion regime. We derive the Green functions for this process using the time-domain collision method, for partial collisions, in which the four fields interact at the beginning or the end of the fiber, and complete collisions, in which the four fields interact at the midpoint of the fiber. If the Green function is separable, there is only one output Schmidt mode, which is free from temporal entanglement. We find that nonlinear phase modulation always chirps the input and output Schmidt modes and renders the Green function formally nonseparable. However, by pre-chirping the pumps, one can reduce the chirps of the Schmidt modes and enable approximate separability. Thus, even in the presence of nonlinear phase modulation, frequency conversion with arbitrary pulse reshaping is possible, as predicted previously [Opt. Express 20, 8367-8396 (2012)].