Complex sentence: The Emperor nominated his eldest surviving son, Mirza Mughal, to be commander in chief of his forces, but Mirza Mughal had little military experience and was treated with little respect by the sepoys.
Split into simpler sentences: The Emperor nominated his eldest surviving son, Mirza Mughal, as the commander in chief of his forces. However Mirza Mughal had little military experience and was rejected by the sepoys.