This follows The Bone Dolls Twin, which is first in the Tamir trilogy by Lynn Flewelling.
There is a third book in the series, The Oracle's Queen, which I hope will be added soon.
Prophecies of old say that Skala will prosper as long as a queen of the true lineage holds the throne. But for many years, a usurper king has ruled, with tragic and devastating consequences for the people. Moreover, keeping the rightful future queen safe directly beneath the eyes of her deadliest enemies is the sacred mission of Skala's renegade wizards. To fulfill that intent, they magically changed the infant girl's body to that of a boy. Eventually shown her true, female face, Tobin is shocked and confused but struggles successfully to navigate "his" complex world, rife with secrets, assassins, and political agendas, and to come to terms with her destiny, which he isn't at all sure he wants. Ultimately, orphaned Tobin must betray his only remaining family and reveal them for the conniving traitors they are. That is a difficult enough task, but Tobin's most bizarre secret must yet come to light before she can claim the throne. A beautiful, compelling, dark tale.