Based on the Simplified Differential Equations approach, we present results for the two-loop non-planar hexa-box families of master integrals. We introduce a new approach to obtain the boundary terms and establish a one-dimensional integral representation of the master integrals in terms of Generalised Polylogarithms, when the alphabet contains non-factorisable square roots. The results are relevant to the study of NNLO QCD corrections for W, Z and Higgs-boson production in association with two hadronic jets.