Hi John,
Those are some very interesting changes that you have picked up in the spectrum of CH Cygni. If you are correcting the spectrum for instrumental and atmospheric response then there is no need to normalise it. In fact those corrections are better than normalising the spectrum. The bumpy spectrum is that of the red giant in the system. Rather than a smooth continuum it has absorption bands, almost certainly due to titanium oxide in the star’s atmosphere.
For comparison here is a spectrum I took on 6th August.
Best wishes,
Andy