FWIW, I run into a similar problem with epub exports from InDesign v4, where for example every ID4 style which specifies "text color black" will, in the epub stylesheet's corresponding style, contain "color:rgb(0,0,0);" I deal with this by just removing or commenting out these statements.
That seems to allow the style to inherit whatever the reading system's default is, I suppose, thus working for both day and night mode.
Perhaps you could make an analogous style definition for "a" in your stylesheet. I.e. don't specify ANY color, and let it take the system defaults, which should be aware of the overall environment.
"When in doubt, take the defaults."
Albert
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