Have you tried Tools > Update DHTML effects in topics? That sometimes cures the weirdest things.
Are you positive that the same classes apply in html before and after reapplying the style? Do the topics use the correct CSS file to begin with? (I'm guessing here to determine why it is going wrong.)
When Rh imports, it creates a CSS for the topics created. If later in the process you are specifying a specifc CSS, things will go wrong as that CSS will have different style names. See Importing on my site. It's not a quick read but I think it will be the answer.
See www.grainge.org for RoboHelp and Authoring tips