I am not sure but i think Structure Sketcher is a JChem extention thats why I am posting it here.
1. Create a Structure Sketcher Node.
2. Open it.
3. Draw something.
4. Try to create a new sketch with the "blank sheet" Icon on the top left.
5. He will ask you "Do you want to save it?".
6. Press "No".
Usually he should discard your not-wanted file now. But it dont will discarded if you press "No". So the only way is to delete the Node and create a new.