KB001297: What are the Steps to the Save Reagent Valve Selection in the 5975 MS Tune File? - MS ChemStation 

The change of Reagent gas from A to B or vice versa will not be captured in the Tune file if you select the reagent gas from the Instrument control menu item or the menu item in the tune view.
With the CI tune wizard the change of reagent gas parameter data will be saved correctly in the tune file.