Of course you should reply. How could you ever initiate anything if you don't?
Taking actions is the mans role. She gave you a small hint, it could be nothing, but it's enough for you to start acting like a man.
Being a player and letting the chick come to you is one thing. Not ceasing the moment is another, and that's what you're doing. By not replying you are not being a "jerk" in her head. You are just being boring.
JPlaya said:
She said you should let me know what i miss in class tomorrow. That kind of sounds like a command.
The word "should" implies it's a hint, not a command.
Just like Jack Sparrow says, don't make a big deal out of it - reply and see what happens. Tell her something like that she missed your company, or make a joke about that you had a test.