We study the merging and splitting of quasi-two-dimensional Bose-Einstein condensates with strong dipolar interactions. We observe that if the dipoles have a non-zero component in the plane of the condensate, the dynamics of merging or splitting along two orthogonal directions, parallel and perpendicular to the projection of dipoles on the plane of the condensate, are different. The anisotropic merging and splitting of the condensate is a manifestation of the anisotropy of the roton-like mode in the dipolar system. The difference in dynamics disappears if the dipoles are oriented at right angles to the plane of the condensate as in this case the Bogoliubov dispersion, despite having roton-like features, is isotropic.