Perhaps in a future DTI novel, an investigation will show a temporal incursion or something caused changes in history involving the characters surrounding the events of IFM? In time, the waves caused by this will dampen out, I'm sure.
BTW, Christopher has mentioned the disappearance of the USS Intrepid in another thread and, as mentioned, DRG mentioned elements of IFM in his last two books. Plus, in one book Geordi's being demoted back to Commander was mentioned. So some elements of IFM are surviving into continuity. When you consider the errors of continuity in episodes of Star Trek, the issues here are extremely minor. Plenty of readers enjoyed IFM, myself included. I hope having been paid, receiving appreciation from fans, and having at least parts of his work survive into the overall story provides Magpie with comfort and a sense of fulfillment. As readers and lovers of Trek, we got a good story and have elements of that book which we know "happened" so we can feel like the money and time we spent on the book was well spent.