We study theoretically the temporal shaping effects experienced by a one-photon wavepacket propagating in a one-dimensional waveguide containing a two-level atom. We show that the transmitted field distorts such that its pulse area (time integral of electric field amplitude) vanishes. As a consequence, specific pulses with initial zero pulse area are shown to be robust with respect to propagation whereas pulses with initial non-vanishing pulse area are shown to be more sensitive, leading to significant distortion after propagation.