How does Matilda know in Chapter 23 that Nathaniel is still alive?

She sees someone pushing flowers through a cracked-open window and scattering them around and then she notices him moving.

Explanation:

Delightedly, she realizes that they are being scattered by Nathaniel Benson, who has evidently survived the fever outbreak and is still thinking of her.

She looks up and sees someone pushing flowers through a cracked-open window. She realizes it's Mr. Peale's house. After the window closes, she sees a tall, lean shadow moving and smiles at the memory of Nathaniel - "He was alive and still sending me flowers."

he was sending her secret messages

Explanation:

As they're walking down the street, Mattie notices that daisies are floating through the air. She looks up and sees someone pushing flowers through a cracked-open window. She realizes it's Mr. Peale's house. After the window closes, she sees a tall, lean shadow moving and smiles at the memory of Nathaniel-"He was alive and still sending me flowers."

Mattie is further heartened by an apparent secret message from Nathaniel, who's quarantined at the Peale house. She has reason to hope that life might regain some normalcy after the epidemic passes.