We present a multi-instrument multiscale study of a channel of enhanced, inhomogeneous flow in the cusp ionosphere occurring on November 30, 2014. We provide evidence that strong Global Navigation Satellite System (GNSS) phase scintillations indices (> 0.5 rad) can arise from such events, indicating that they are important in the context of space weather impacts on technology. We compare in detail two-dimensional maps of ionospheric density, velocity, and temperatures obtained by the European Incoherent Scatter Scientific Association Svalbard Radar with scintillation indices detected from a network of four GNSS receivers around Svalbard and examine the different sources of free energy for irregularity creation. We observe that the strongest phase scintillations occur on the poleward side of the flow channel in a region of sheared plasma motion and structured low-energy particle precipitation. As inhomogeneous plasma flows are evident in our observations, we perform a quantitative, nonlinear analysis of the Kelvin-Helmholtz instability (KHI) and its impact on phase scintillations using numerical simulations from the first principles-based Geospace Environment Model of Ion-Neutral Interactions and Satellite-beacon Ionospheric-scintillation Global Model of the upper Atmosphere. Using representative values consistent with the radar data, we show that KHI can efficiently create density structures along with considerable scintillations and is thus likely to contribute significantly under similar conditions, which are frequent in the cusp.