We present analysis of observational data from the Swift Burst Analyser for a sample of 15 short gamma-ray bursts with extended emission (SGRBEEs) which have been processed such that error propagation from Swift’s count-rate-to-flux conversion factor is applied to the flux measurements. We apply this propagation to data presented by the Burst Analyser at 0.3-10 keV and also at 15-50 keV, and identify clear differences in the morphologies of the light-curves in the different bands. In performing this analysis with data presented at both 0.3-10 keV, at 15-50 keV, and also at a combination of both bands, we highlight the impact of extrapolating data from their native bandpasses on the light-curve. We then test these data by fitting to them a magnetar-powered model for SGRBEEs, and show that while the model is consistent with the data in both bands, the model’s derived physical parameters are generally very loosely constrained when this error propagation is included and are inconsistent across the two bands. In this way, we highlight the importance of the Swift data processing methodology to the details of physical model fits to SGRBEEs.