Follow this step by step...
1. When the New Mutants were killed by the Beyonder and then revived... what if they were revived with different memories..?
2. What if the whole Earth was killed and then revived with different memories?
3. What if the whole Earth was killed and some weren't revived, and they were replaced with characters that had long been dead, all with different memories to match the current status quo?
4. What if they weren't killed but just 'willed out of existence'?
Now... if you made it this far...
Did the past before the change still exist?
I think if you're outside the bubble it would go pre-change - change - post-change.
But if you're in the bubble, you can only see the post-change, which has a history that extends into the time that was previously only in the pre-change.
And if you were in the bubble, you'd believe the post-change is all there is.
But if you somehow made your way out of the bubble you would see that the post-change really had no history and you'd see what existed before the change.
Now, think of Psylocke's trip through the Siege Perilous.
Since the world didn't change, to the X-Men and everyone else she had a history separate than what she believed.
When people write about her in bios, it goes: history of Psylocke prior to the Siege Perilous then the effects of her trip and then her new existence afterwards.
The reason being that the world of the X-Men didn't change, just Psylocke.
However, if it was written from Psylocke's POV, or if the whole world had gone through the Siege Perilous, there would have been nothing to relate that there was anything ever before that was different.
Then you'd get Version 1 and Version 2 of Psylocke because there would be nothing connecting the two.
Now, imagine Zero Hour.
The last universe faded out of existence with the last panels of every comic being blank.
The next month, all the books continued on as if nothing ever happened, at least in their minds.
Now, the question is... which origin (of Character A) is correct?
The answer is... the one they remember, unless someone from the previous reality still exists and remembers one that's different. (Well, unless you're Psycho-Pirate and no one believes you because you're labeled crazy.)
Then that one supercedes the origin the character, themselves, remember. They just don't remember it. But it is still their origin.
However, if no one remembers the previous reality then Character A's origin is the one they remember and that's referenced by those around them.