How to reproduce:

Open the “IN-149182” project
In the Project tab, open “Assets/New Graph._mygraph”
In the Graph Editor window, right-click on empty space > “Add Node” > “MyContext”
In the Graph Editor window on the “MyContext” node > “Add a Block” > “MyBlock”
Save “Assets/New Graph._mygraph” (Ctrl + S)
In the Project tab, open “Assets/Editor/MyNodes.cs”
In code editor, change both the “class MyContext” declaration and the “[UseWithContext(typeof(MyContext))]” reference to “MyContext2” and save the file (Ctrl + S)
In the Graph Editor window, right-click the “Missing Node” > “Delete”
Observe the results in the Graph Editor window and in the Console

Actual result: Deleting the “Missing Node” throws “NullReferenceException: Object reference not set to an instance of an object” in the Console, and the node is not deleted
Expected result: The “Missing Node” is deleted without any errors in the Console

Reproducible with: 0.1.0-exp.1 (6000.2.0a9), 0.4.0-exp.2 (6000.2.0a9), 6000.5.6f1, 6000.6.0b6, 6000.7.0a3
Could not test with: 6000.0.80f1 (Graph Toolkit package not available), 0.4.0-exp.2 (6000.3.21f1) (crash when adding “MyBlock”)

Reproducible on: Windows 11 Enterprise (25H2)
Not reproducible on: No other environments tested

Workaround: Rename the class and [UseWithContext] reference back to the original name and save the script - the type resolves again and the node can be deleted normally