In the last update, has "clear highlighting" now gone missing? If I mark a passage, I cannot find the means/button to clear all highlighting any more either.
That is very strange, but yes, it does appear to have gone missing. In the meantime, you can use Cmd+Shift+K to clear the highlighting (and Cmd+K to apply the currently selected style to a selection).
I've posted a bug in our bug tracking database and we'll look at this before the next release.