The diffusion bonding technique has many applications in non-linear frequency-conversion processes. Unfortunately, when used for bonding periodically poled crystals, the periodic patterns have to be very precisely matched for efficient conversion. We investigated theoretically and experimentally this effect, in two configurations of increasing the length or the thickness of a crystal. We found that the sensitivity to the relative periodic domain match is much more severe for the case of increasing the crystal length with respect to increasing its thickness. Furthermore, even for symmetric pump illumination with respect to the interface between two crystals, an asymmetric intensity distribution may be obtained in the second harmonic. We have experimentally measured the second harmonic power modulation caused by varying the relative domain match at the interface between two attached, but unbonded crystals. A novel configuration for the domain patterns is proposed, which limits the degradation of the generated light caused by the domain mismatch.