How to reproduce:

Open the attached "IN-150883_NewHierarchyTest.zip" project
Open the "SampleScene" located in the Scenes folder
Select the "Control" GameObject in the Hierarchy tab
In the Inspector, change the Flags dropdown in the Control (Script) component to "HideAndDontSave"
Observe the Hierarchy
Press Ctrl+S/Cmd+S and completely reopen the project
Observe the Hierarchy and the Console

Actual result: The "Target" object's text turns gray, but the object remains visible in the Hierarchy list, after reopening the project, the object disappears from the Hierarchy, but errors are thrown in the console
Expected result: The "Target" disappears from the Hierarchy immediately upon changing the flag to "HideAndDontSave", without throwing any console errors or requiring a project reopen

Reproducible with: 6000.3.0a2, 6000.3.23f1, 6000.5.10f1, 6000.6.0b10, 6000.7.0a5
Could not test with: 6000.0.0f1, 6000.0.82f1, 6000.3.0a1 (The New Hierarchy (Hierarchy V2) feature is not available in these versions)

Reproducible on: Windows 11
Not reproducible on: No other environments tested

Workaround: Navigate to Edit -> Preferences -> General and disable “Use new Hierarchy window”

Notes:

The first line of the error messages is “UnassignedReferenceException: The variable Target of Control has not been assigned.”
In 6000.3.23f1 specifically, step 5 does not even turn the text gray (nothing visually changes at all) until Ctrl+S/Cmd+S is pressed