Search and replace of css isn't possible as you noted. However in practice most books I've seen don't explicitly set font colors. For these cases you can use extra css and set font-color and background color on the body or page element. This will take care of most books during conversion.
It's just books that do have specific colors set that would still be a problem - the extra css feature can potentially override these too, but you need to know which selector to apply the setting too. @body or @page is probably too broad, so you'd need to go to p or whatever.
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