Look behind you, a three-headed monkey!
Sorry--I guess I'm one of the only people who remembers, years ago, when mere mention this topic would mean a terrible flame war. I guess we're... growing up?
Damned shame.
To be perfectly clear, the idea that ship you know as the Dragon is 'really' (or:
secretly) the Lance is a 'retcon' in the most basic sense. It is a fact 'added' by the game's novelization. Wing Commander IV and all of its documentation and the Origin's Official Guide to Wing Commander IV all call it only the 'Dragon' (as would have any of Origin's behind-the-screens material--the script, production drawings, internal files, etc.) There was no plan on the part of the game development team to call the ship anything but the Dragon.
The novel introduces the backstory discussed above: the ship's official name is 'Black Lance' and the ones flown by the GE pilots in Wing Commander IV are frequently assigned the (mission) callsign 'Dragon' (yes to the above, similar to how Casey might be 'Alpha Leader' in Wing Commander Prophecy). Here is the exact quote: "
'We cracked open a box of technical tapes,' Pliers said, 'that's what they call 'em. Black Lances. Callsign's usually Dragon.'" The book then goes on to refer to them as Lances or Black Lances throughout.
That's not an unreasonable retcon, really. I can't speak to Dr. Forstchen and Mr. Ohlander's intentions, but I do know that aspects of Wing Commander IV bothered the former and I can make some educated guesses. I think they decided it all sounded a little silly: Tolwyn is now an unrepentant Nazi and he has an evil organization no one has ever noticed with an evil name (and SS logo!) and their own special fighters that have evil names. With a little bit of tweaking they managed to create a bit more versimilitude without hurting what was already spoken in the game. 'Lance' sounds a lot more like an existing Confederation development co-opted by Tolwyn's project, it's the source of the organization's /internal/ nickname (the name is formalized as The Project or the 212th in the book) and so on.
(Also, remember that the novelization was written based only on the game's shooting script... which itself included an interesting bit never made clear in the finished game: the fighter in question is supposed to be recognizable as an evolution of the Excalibur program. I get the distinct feeling the that particular line of scene-setting had a lot to do with the decision to create the further backstory.)
Anyway: yes, it's a retcon and it's one that should only be known by extreme Wing Commander nerds. You have to have read the novelization to know about the change... which is a tiny fraction of people who played the game. Even if you have read the book, you have to give it some credence, too--the novel was published in October, 1996 and the game came out in February... so there was half a year when fans called it nothing but 'Dragon', no matter how anal they were.
It's not a problem with retcons in general, they're an entirely normal thing in fiction--if we'd had many more stories after Wing Commander IV I'm sure we'd all know about the 'Lance' thing just like we learned Blair's name or which Tiger's Claw pilots "really" died. It would have filtered down since it was part of the "canon" that stories set after 2673 might mention... but although there were plenty of Wing Commander stories released after Wing Commander IV, very few were actually *set* then. It's kind of surprising to think about it, but the TV show, the movie, every novel except the bookends of Action Stations, etc. all took place in earlier years and so had no need to mention the fighters again.
Secret Ops touches on the name obliquely by introducing the fact that the Confederation's uprated "covert ops" versions of fighters are, indeed, named 'Black' so-and-so ('Black Wasp', 'Black Vampire', etc... and thus both the 'Black Lance' and the 'Black Hellcat' in the WC4 novelization refer to the fact that they're the covert versions of those spacecraft.) The Wing Commander Arena booklet finally gives us the fighter's designation (and suggests that there may be a plain 'Lance' version).