How can a sum of money taken from the school to buy stories for students be returned, after two years have passed, and fearing that the current principal might find out?

Your sister must seek forgiveness and return what she took to the school without informing the principal if she fears harm. The important thing is for the right to reach its rightful place so that her conscience may be cleared. If she took the amount under duress, there is no sin upon her, but she must return it, for the Prophet, peace and blessings be upon him, said: "The hand is accountable for what it takes until it returns it."