(The same answer as Andrew but with a bit more detail,read and forget if you like!)
Your measurements are showing nice qualitative trends but you have to be a bit careful when interpreting the EW of emission lines.
EW works well as a measurement of absorption line strength because absorption is normally just a proportion of the continuum, so provided you can decide where the local continuum is, the EW gives you a good measurement of the line strength. (eg even if the star changes in brightness, if the absorption is constant, the EW stays the same.)
Emission lines are different as they normally come from a different source than the continuum so are independent of it. This means the EW value of an emission line makes less sense as we are measuring it relative to something not connected with the emission line. This is OK provided we know that the continuum flux is constant (or at least how it is changing, so we can correct the EW to give a true measurement of the line strength) Otherwise the EW results can be deceiving. Classical novae are a good example. If you plot the EW of H alpha as the nova evolves it looks like the line is continuously getting stronger. In fact though this is mainly due to the continuum falling away and for much of the time the actual line strength is constant and even decreasing at times.
If we look specifically at your VV Cep spectrum, the hot star is now fully eclipsed so the continuum is that of the cool star photosphere and the emission comes from somewhere else (possibly an extended region (disc?) associated with the hot star but there are many possible sources). The variations in the continuum around the emission line will be due to a blend of the many absorption lines in the cool star spectrum and we don’t see the true continuum at this resolution (It will likely be somewhere along the high points of the spectrum). The reference points you have chosen will be somewhere in the absorption lines so will only be fixed during totality, assuming no variations in the cool star spectrum. Outside totality, the reference points will rise closer to the continuum level as the hot star reappears and the cool star absorption lines lose their relative strength. The continuum flux will also increase to that of the two stars combined. Both these will affect the EW measurement even if the emission line strength actually remained constant.
All is not lost though if you want to make an absolute measurement of the way the emission line flux is varying, as all the necessary information is available.
What we would first need to do is to convert the spectrum to absolute flux. This could be done using the available measurements of photometric brightness around the time of the spectrum. Once that has been done, we can work in absolute flux rather than relative to some poorly defined and varying continuum.
The next step would be to remove the cool star component. We could try this now by subtracting a reference spectrum of a star of the same type, adjusting it to match the intensity of the absorption lines, but probably the best way to do this would be to wait to around mid eclipse when the hot star and any circumstellar material should be hidden and use this as a template. Once this is subtracted, we should be left with the flux calibrated spectrum of the uneclipsed components, probably dominated by Balmer emission lines with their actual intensities measurable directly.