She's totally discounting the possibility of him being one of her ancestors.
Is this some "I'm my own great-great-grandma" kinda thing?
Almost certainly. It would explain why she is disappearing when she moves further away, because that means they're destined fate of giving birth to their own bloodline isn't going to happen.
It could also be something a little more convoluted, like their child saves the life of a woman who is an ancestor of the FMC -- a butterfly flaps it's wings type of scenario.