Magnetic skyrmions are particle-like, topologically protected magnetization entities that are promising candidates for information carriers in racetrack-memory schemes. The transport of skyrmions in a shift-register-like fashion is crucial for their embodiment in practical devices. Recently, we demonstrated experimentally that chiral skyrmions in Cu2OSeO3 can be effectively manipulated by a magnetic field gradient, leading to a collective rotation of the skyrmion lattice with well-defined dynamics in a radial field gradient. Here, we employ a skyrmion particle model to numerically study the effects of resultant shear forces on the structure of the skyrmion lattice. We demonstrate that anisotropic peak broadening in experimentally observed diffraction patterns can be attributed to extended linear regions in the magnetic field profile. We show that topological (5-7) defects emerge to protect the six-fold symmetry of the lattice under the application of local shear forces, further enhancing the stability of proposed magnetic field driven devices.