Well in general, if you filter in the Fourier domain, you'd filter the magnitude image only by erasing some part of it, like the high frequency region. I don't think usually you filter the phase image. So that's how it would be affected.
Of course if you filter in the spatial domain, both magnitude and phase parts will be affected. How depends on what kind of filtering was done, but they'll be different than those from an original, unfiltered image.
