Difference in spectrum HD42477/HR2191

Dear spectroscopists,

I could do with some advice. Recently I imaged 32 Gem and used HD42477 as reference to get the instrument response. Being rather dim objects (magnitude 6-6.5) I imaged both on two consecutive nights. I processed the two 32 Gem datasets separately (each with its own NeAr calibration data) and finally stacked both nights to get a single 1D profile. Meanwhile I am advised not to stack spectroscopic data obtained on different nights, and looking at my data of the reference star I now understand why:

The graph shows both target 32 Gem and reference star HD42477, data from both nights (only wavelength calibrated, no IR yet, 2400lpmm grating, 20 micron slit, ZWO ASI2600MM Pro and modified MLAstro SHG700 behind Celestron C11 EdgeHD). As you can see the data of 32 Gem (blue and green) of both nights match pretty good in intensity, but that of the reference star (red and purple) do not (apart from the section above 685nm).

Problem is that I do not understand why they differ that much. Prior to taking calibration and light frames my script also takes a snapshot of the sky where the scope is pointing at and on both nights the same reference star was imaged.

Can this be due to thin cloud cover during acquisition of the purple line? If so, why is that not affecting the whole wavelength range (and not 32 Gem)?

Or is this due to variability in HD42477? It is a type A0Vnne star, which means it basically is a rapidly rotating A‑type Be‑like star. I also found that it is a pulsating star, but wonder whether that could cause these differences?

I used the reference star profile of the first night (the red line) to determine the instrument response for both 32 Gem profiles (and thus for the stacked 1D profile), but am unsure whether that was a good idea. The data in the graph is not yet instrument response corrected.

Thanks for your thoughts and
kind regards,
Nicolàs

To further on my previous post: last evening I collected another 5 1200s subs of HD42477 to see the effect of yet another observing night (again no IR applied).

I kept the colours of the previous two recordings and added the new data as orange line to the graph. In shape it is quite similar to the red line in the graph, although above 690nm it clearly starts to deviate.

Nicolàs