The difference between the two is that one includes a direction of up.
Let's say you had an aunt that lived in the north of your country, and you lived in the south. You could say:
My aunt from the north of the country came to visit me.
Or you could include the detail that she lives in the north simply by adding the direction:
My aunt came down to visit me.
In case this is not familiar to you, it is common in English to speak of travelling up from the South, or down from the North. By adding in the direction she travelled you are also indicating, albeit vaguely, where she came from.
Likewise in your example, saying that "her head came back up" indicates to the reader that her head was down to begin with. The word "back" alone merely means to return to the position it was in before. You could just as easily say "her head came back down".