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Compared to isotropic liquids, orientational order of nematic liquid crystals makes their rheological properties more involved, and thus requires fine control of the flow parameters to govern the orientational patterns. In microfluidic channels with perpendicular surface alignment, nematics discontinuously transition from perpendicular structure at low flow rates to flow-aligned structure at high flow rates. Here we show how precise tuning of the driving pressure can be used to stabilize and manipulate a previously unresearched topologically protected chiral intermediate state which arises before the homeotropic to flow-aligned transition. We characterize the mechanisms underlying the transition and construct a phenomenological model to describe the critical behaviour and the phase diagram of the observed chiral flow state, and evaluate the effect of a forced symmetry breaking by introduction of a chiral dopant. Finally, we induce transitions on demand through channel geometry, application of laser tweezers, and careful control of the flow rate.