Pollen species are distinguished by shape and color. pollen often contains pigments which gives color. But during acetolysis (Acid digestion) only exine wall remains as it is. Depending upon acetolysis time (actually due to sulfur ion attachment) pollen appear as pale brown to dark brown color after acid digestion. To color the pollen after acetolysis, better way to mount pollen in Glycerin jelly with saffranin (red color) or methyl green (Green color), pollen appeared distinctly.
Sometimes pollen color after acetolysis also depending upon the exine thickness. For instance echinate pollen (with thick exine) commonly becames very dark after acetolysis, in that case a chlorination is necesary to get more detailes analysis.
Pollen color after acetolysis usually do not remain the same. However using Glycerin jelly with saffranin gives them an added red coloration. But know it that add more may obstruct some of the important features such as the ornamentation
I argue; to get a detailed picture of the pollen grains, If staining can reduce the results of the analysis, how about using a contrasting colored lenses as background when observed under a microscope.