I would say pa liw ydy'r baner cymru, though I suppose I should use the exact wording of the question ...
Do you need the 'r there?
I would have thought that baner Cymru would be definite by default, since Cymru (a proper noun) is definite.
I think they did it that way because "baner" is feminine, and they don't want to confuse you with the mutation.
I think you did use the exact wording... pa/which liw/colour ydy'r/is the baner/flag cymru/of wales
That would make sense but it is an incorrect translation of the sentence given.