Comic!
This is a complicated question, actually. The person that the female MC THINKS is the Big Bad, she DEFINITELY knows, to the point that she spends decades hunting him down. The person she thinks is the Big Bad definitely recognizes her as a thorn in his side, but to him, she's a medium-sized annoyance, whereas for her, vengeance against him is one of her main motives. (Turns out, he isn't even close to the Biggest, Baddest thing that happens to her. He's just the catalyst that starts her journey.)
None of this has happened in the actual comic thus far, as I'm only on page 5 (of 7) of the prologue... but it will!