Concerning the change in wavelength (and hence change in lattice constant) due to the refractive index of the gas, this effect is tiny. We consider it in section 6, on p17 and show that the correction to the refractive index is of order 10^-9 for our parameters. This is to be distinguished from the effective change in the cavity length which, due to the resonance effect, is substantial and is precisely what lies behind the amplitude modulation of the lattice.
Also the BEC will lead to an effective change of the cavity length and lattice constant, which should renormalize the wavelength and thus om_recoil.