I understand from Voyages of the Imagination and also from other sources that A Flag Full of Stars was significantly changed from original manuscript to published form. I understand that Brad Ferguson doesn't really feel that it is "his" work any more - sounds like a similar situation to what happened with Probe. I wonder if there is more information somewhere about the original content of the novel.
Ferguson used to have a link to a PDF of his version of AFFoS
available on his website. I downloaded a copy years ago (maybe 10 or more...)
I've managed to snag copies of the author's drafts of a couple Trek
novels. They make an interesting read, when compared to the final, published versions.