This happened because you deleted a model from diagram
, not from the project.
In Astah, there are two ways to delete models.
Delete from Model
Deletes selected model completely from the project file and from all the diagrams.
Delete from Diagram
Removes selected model from a currently-open diagram. Model itself stays in the project file. So it appears in the tree view, property view and on other diagrams.
Using the shortcut key would be faster and make less mistakes at delete.