It is hard (for me at least) to find out with any certainty what units carried what flags in the Continental Army; Guilford is no exception.
The 3rd Maryland carried a "Besty Ross" style flag at Cowpens, with an additional star in the center of the circle of stars. So that flag might be a possibility. There are pictures of an American Guilford Courthouse flag, an interesting adaptation of the Besty Ross. It has red and blue stripes and a white background for the stars in the corner. This may have been a militia flag or maybe Green's flag???
So for my Continentals at Guilford I plan to go with the standard Besty Ross style, although if I can find a GMB flag for Maryland Regiment at Cowpens then I will use that one too not to mention the Guilford flag.
Good luck with the armies. Guilford is my next project. If you are interested in Guilford I suggest you get "Long, Obstinate and Bloody." It is the best study on the battle I have read.
Mike B