Yes the acid test is to rerun the reference star using the calculated instrument response
If the flat has done its job well the instrument response should be nice and smooth (just the flat lamp spectrum and atmospheric extinction plus any wavelength selective sampling at the slit due to chromatism) I am not sure if BASS does this but ISIS even assumes a black body curve for the flat lamp so in theory with ISIS ideally all you should be left with is the atmospheric extinction. With my LHIRES at H alpha high resolution this results in a dead flat instrument response within a couple of percent every time so it is hardly worthwhile doing an instrument response correction. In practise with my ALPY there are some small ripples at a couple of percent from the sensor response which the flat has not quite dealt with and a rather nasty kink to deal with around 4000A. I am not sure where it comes from but others have also reported it. Perhaps the reflectivity of the paint used on the reflector used in the ALPY calibration module ? Note the variation in shape in this collection of my IR curves. A lot of this I believe is due to chromatic aberration in my focal reducer coupled with slight differences in focus.