We present an improved, hybrid CPU-GPU atmospheric retrieval code, Helios-r2, which is applicable to medium-resolution emission spectra of brown dwarfs, in preparation for precision atmospheric spectroscopy in the era of the James Webb Space Telescope. The model is available as open-source code on the Exoclimes Simulation Platform. We subject Helios-r2 to a battery of tests of varying difficulty. The simplest test involves a mock retrieval on a forward model generated using the same radiative transfer technique, the same implementation of opacities, and the same chemistry model. The least trivial test involves a mock retrieval on synthetic spectra from the Sonora model grid, which uses a different radiative transfer technique, a different implementation of opacities, and a different chemistry model. A calibration factor, which is included to capture uncertainties in the brown dwarf radius, distance to the brown dwarf and flux calibration of the spectrum, may compensate, sometimes erroneously, for discrepancies in modeling choices and implementation. We analyze spectra of the benchmark brown dwarf GJ 570 D and the binary brown dwarf companions in the Epsilon Indi system. The retrieved surface gravities are consistent with previous studies and/or values inferred from dynamical masses (for Epsilon Indi Ba and Bb only). There remains no clear criterion on how to reject unphysical values of the retrieved brown dwarf radii. The inferred radii and corresponding masses should be taken with great caution. The retrieved carbon-to-oxygen ratios and metallicity depend on whether chemical equilibrium is assumed.
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