We present an internal-flow multiscale method ('unsteady-IMM') for compressible, time-varying/unsteady flow problems in nano-confined high-aspect-ratio geometries. The IMM is a hybrid molecular-continuum method that provides accurate flow predictions at macroscopic scales because local microscopic corrections to the continuum-fluid formulation are generated by spatially and temporally distributed molecular simulations. Exploiting separation in both time and length scales enables orders of magnitude computational savings, far greater than seen in other hybrid methods. We apply the unsteady-IMM to a converging-diverging channel flow problem with various time-and length-scale separations. Comparisons are made with a full molecular simulation wherever possible; the level of accuracy of the hybrid solution is excellent in most cases. We demonstrate that the sensitivity of the accuracy of a solution to the macro-micro time-stepping, as well as the computational speed-up over a full molecular simulation, is dependent on the degree of scale separation that exists in a problem. For the largest channel lengths considered in this paper, a speed-up of six orders of magnitude has been obtained, compared with a notional full molecular simulation.