Most of the time I have observed that Id/Ig ratio increases after reduction of GO and and Ad/Ag ratio decreases [where A denotes area under the peak]. Could you please help me by sharing your idea D peak's intensity increases after reduction.
I believe that it is correct to use the area instead of the height of the peak. The area can better be obtained after fitting but it needs care how many peaks to use in the fit. Most probably, after reduction, the shape of the peak changes and this causes the disagreement between the height and the area ratios.
In the case of each band one has two parameters: height (Intensity) and FWHM (Full Width at Half Maximum). If you want to analyze the behavior of your spectra you should take into account both parameters. The are somehow combine bot parameters into one. To have the chance to suggest something more precise I need to have a look at your spectra.
I am waiting for publicate my work, in which i described all bands for disordered, oxidized graphite based materials. Additionally, I present simple method fitting Raman spectra and analysis of obtained components. If you want, i will send you it when this article will be "in press". Actually it was send to production :).