- The data was not removed when she left.
There doesn't seem to be any need for past-perfect in this situation. One thing happened in the past ("she left") and the other didn't happen at all.
That is, it didn't happen when it should have happened (when she left, or immediately after).
The sentence leaves open the question of whether the data might have been removed more recently.
To clarify that, add one of these:
. . . but it has been removed now.
. . . but it was removed on {date}.
. . . and it still hasn't been removed.