The bulk-edge correspondence (BEC) is the hallmark of topological systems. In continuous (non-lattice) Hermitian systems with an unbounded wave vector, it was recently shown that the BEC of Chern insulators is modified. How would it be further affected in non-Hermitian systems, experiencing loss and/or gain? In this work, we take the first step in this direction, by studying a bulk-Hermitian continuous system with non-Hermitian boundary conditions. We find in this case that edge modes emerge at the roots of the scattering matrix, as opposed to the Hermitian case, where they emerge at its poles (or, more accurately, coalescence of roots and poles). This entails a nontrivial modification to the relative Levinson's theorem. We then show that the topological structure remains the same as in the Hermitian case, and the generalized BEC holds, provided one employs appropriately modified contours in the wave-vector plane so that the scattering matrix phase winding counts the edge modes correctly. We exemplify all this using a paradigmatic model of waves in a shallow ocean or active systems in the presence of odd viscosity, as well as 2D electron gas with Hall viscosity.