I said I'm sorry to bother you. She said it's okay. How should I reply?

You apologize to her politely, and it doesn't matter if she answers you politely. This is the happy ending. What else do you want to say? Unless you have a crush on her, I hope to talk to her more. When she said it doesn't matter, you went on to say, look at her reaction, it's great! If you keep a straight face, it's over. If you smile at me, it's up to you.