The ELISE test facility at IPP Garching hosts an RF-driven negative hydrogen ion source and extraction and acceleration system. Its target is to demonstrate the performance foreseen for the ITER neutral beam injection (NBI) system in terms of extracted current density (329 A m−2 in hydrogen, 286 A m−2 in deuterium), electron-ion-ratio (1) and pulse length (up to 3600 s in deuterium and 1000 s in hydrogen). NBI systems are compromised by a process commonly known as stripping losses (neutralization of negative ions before they achieve full acceleration). According to theoretical estimations, for a source filling pressure of Pa, 29% of the extracted ions are lost by stripping in the ITER full-scale NBI system. Experimentally, stripping losses are monitored using Beam Emission Spectroscopy (BES). Previous experimental measurements of the stripping losses at ELISE yielded values around 1.7%, which were much lower than the 10% predicted for the pre-accelerator system. The notable difference has sparked concern about the conventional interpretation of the BES experimental measurements used at IPP. The Bavarian Beam Code for Negative Ions (BBCNI) is a full 3D particle tracking code that can also produce synthetic BES spectra. BBCNI is used to evaluate how accurately different analysis techniques determine the stripping losses from the BES. This is achieved by comparing the results with the total simulated count of stripping losses. The analysis method that produces the most accurate results is identified and then systematically applied to evaluate ELISE's data from various experimental campaigns. For a nominal source filling pressure Pa an average of 5.8% is measured experimentally when evaluating the data with this method. Although higher than previously determined with BES, stripping losses are still smaller than predicted values. This may open the option to increase the filling pressure in the source as a means to facilitate achieving the targeted ITER conditions.