The align tool does not receive data about moving an object to a new artboard.

[Max N]

The alignment tool receives data about moving an object to a new work area only after deselecting (click with the mouse in free space) from the object.
In the layers panel, the object is already displayed in the new work environment, and the alignment tool continues to center relative to the original work area.
More on the gif below.

[Sean P]

Hi Max, 

This is a known issue that is with development to be fixed. I'll get it bumped with them!