In this work we present a methodology to evaluate the accuracy of methods used to quantify the uncertainty in estimated total energy savings. We focus on savings measurement and verification (M&V) approaches that use a baseline model to characterize energy use, and that forward-project the model for a counterfactual to determine avoided energy use. These approaches are common to the International Performance Measurement and Verification Protocol's (IPMVP's) Option C and Option B. This methodology can be used to evaluate the uncertainty in savings estimates that are due to model error. It has been applied to evaluate two uncertainty estimation methods, including the industry standard ASHRAE Guideline 14 approach. The evaluation used data from 69 commercial buildings and four different baseline models that span daily and hourly granularity, as well as linear and non-linear/non-parametric forms. The findings of this work indicate that the standard methods that are widely used by the M&V community for estimating the total savings uncertainty over the post-installation period tend to underestimate the uncertainty. The tendency to underestimate the uncertainty is stronger for hourly models than for daily models, due to stronger autocorrelation in model residuals at the hourly time scale.