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Abstract Unconditionally stable time stepping schemes are useful and often practically necessary for advancing parabolic operators in multi-scale systems. However, serious accuracy problems may emerge when taking time steps that far exceed the explicit stability limits. In our previous work, we compared the accuracy and performance of advancing parabolic operators in a thermodynamic MHD model using an implicit method and an explicit super time-stepping (STS) method. We found that while the STS method outperformed the implicit one with overall good results, it was not able to damp oscillatory behavior in the solution efficiently, hindering its practical use. In this follow-up work, we evaluate an easy-to-implement method for selecting a practical time step limit (PTL) for unconditionally stable schemes. This time step is used to ‘cycle’ the operator-split thermal conduction and viscosity parabolic operators. We test the new time step with both an implicit and STS scheme for accuracy, performance, and scaling. We find that, for our test cases here, the PTL dramatically improves the STS solution, matching or improving the solution of the original implicit scheme, while retaining most of its performance and scaling advantages. The PTL shows promise to allow more accurate use of unconditionally stable schemes for parabolic operators and reliable use of STS methods.