We investigate bilayer graphene systems with layer switching domain walls separating the two energetically equivalent Bernal stackings in the presence of an external magnetic field. To this end we calculate quantum transport and local densities of three microscopic models for a single domain wall: a hard wall, a defect due to shear, and a defect due to tension. The quantum transport calculations are performed with a recursive Green's function method. Technically, we discuss an explicit algorithm for the separation of a system into subsystems for the recursion and we present an optimization of the well known iteration scheme for lead self-energies for sparse chain couplings. We find strong physical differences for the three different types of domain walls in the integer quantum Hall regime. For a domain wall due to shearing of the upper graphene layer there is a plateau formation in the magnetoconductance for sufficiently wide defect regions. For wide domain walls due to tension in the upper graphene layer there is only an approximate plateau formation with fluctuations of the order of the elementary conuctance quantum σ0. A direct transition between stacking regions like for the hard wall domain wall shows no plateau formation and is therefore not a good model for either of the previously mentioned extended domain walls.