How does Scathach come back in The Sorceress The Secrets of the immortal Nicholas Flamel?

No.

Scathach is dragged into the river in Paris by Dagon, who is Machiavelli's driver/assistant/friend who wanted revenge on Scatty. Scathach is still alive and makes her reappearance towards the end of "The Sorceress" with minor cut's and bruises.

Dagon is also still alive.