I think you may have slightly confused what happens in this story. Helen Stoner actually hears the strange whistle at night twice before she comes to Sherlock Holmes. The first time she heard it, as she narrates to Sherlock Holmes and Dr. Watson, was the night when her sister died. After hearing her sister's cry, she rushes out to go to her, and note what she says happened:
I sprang from my bed, wrapped a shawl around me, and rushed into the corridor. As I opened my door I seemed to hear a low whistle, such as my sister described, and a few moments later a clanging sound, as if a mass of metal had fallen.
Previously, Helen's sister had asked Helen if she had heard a whistle during the night. Thus it is that Helen associates this whistle with her sister's death and the terror that she evinced before her final breath. Of course, now that Helen herself has heard the whistle at night, she shares that same terror of the mysterious fate that befell her sister, and has come to Sherlock Holmes to ask him to investigate.