Abstract: Bilayer graphene can exhibit deformations such that the two graphene sheets are locally detached from each other resulting in a structure consisting of domains with different van der Waals inter-layer coupling. Here we investigate how the presence of these domains affects the transport properties of bilayer graphene. We derive analytical expressions for the transmission probability, and the corresponding conductance, across walls separating different inter-layer coupling domains. We find that the transmission can exhibit a valley-dependent layer asymmetry and that the domain walls have a considerable effect on the chiral tunnelling properties of the charge carriers. We show that transport measurements allow one to obtain the strength with which the two layers are coupled. We perform numerical calculations for systems with two domain walls and find that the availability of multiple transport channels in bilayer graphene significantly modifies the conductance dependence on inter-layer potential asymmetry.