I would have to say that Hannah represents the crux of the conflict in Yolen's work. She is a modern teen at the outset of the novel who is driven by a desire to be cosmopolitan and cannot understand the relevancy of her ancestors' struggle. When she opens the door for the prophet Elijah, she enters into the major conflict of the work. From someone who has no care about what it means to be Jewish, she becomes someone who is immersed in the middle of the Holocaust and must reconcile her prior feelings about her race with the realities that race faced. I think within Hannah we see the crux of the conflict in the Holocaust, a setting where individuals had to choose between standing up for the trampled rights of others versus silence and apathy. Just as Hannah endures this conflict, so did the historical victims of the Holocaust. Her struggle ends up mirroring the struggles of her people.
The main conflict for this book is the Holocaust. It is the unfair and deplorable treatment of the Jewish people in Nazi Germany. They are sent to concentration camps and killed via gas chambers.
If you are talking about the main conflict for the main character (protagonist) it is the fact she is not appreciating her Jewish ancestry and therefore is transported back in time to the Nazi era and becomes Chaya. The conflict becomes her struggle to survive, and ultimately... does she?
So depending on how you approach the novel, a historical context or for a character, there are two major conflicts. In some ways they secondary character conflict is obsorbed into the larger historical contextual conflict.