The characterization of errors in a quantum system is a fundamental step for two important goals. First, learning about specific sources of error is essential for optimizing experimental design and error correction methods. Second, verifying that the error is below some threshold value is required to meet the criteria of threshold theorems. We consider the case where errors are dominated by the generalized damping channel (encompassing the common intrinsic processes of amplitude damping and

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... asing) but may also contain additional unknown error sources. We demonstrate the robustness of standard T_1 and T_2 estimation methods and provide expressions for the expected error in these estimates under the additional error sources. We then derive expressions that allow a comparison of the actual and expected results of fine-grained randomized benchmarking experiments based on the damping parameters. Given the results of this comparison, we provide bounds that allow robust estimation of the thresholds for fault-tolerance.