How do I correctly edit an object in another scene?

I am using additive scenes, then have an editor function to modify a property an another object inside a different scene.

However, it's not saving the change when I hit play!!

Here's the code:

             var units = GameObject.FindObjectsOfType<BaseUnit>();
             foreach ( var unit in units )
             {
                 if ( unit.IsFirstPickUnit == true )
                 {
                     unit.IsFirstPickUnit = false;
                     if ( !Application.isPlaying )
                         EditorSceneManager.MarkSceneDirty( unit.gameObject.scene );
                 }
 
             }

But it doesn't work! The scene is correctly marked dirty, but the unit's flag is NOT changed.

So I tried this next:

             var units = GameObject.FindObjectsOfType<BaseUnit>();
             foreach ( var unit in units )
             {
                 if ( unit.IsFirstPickUnit == true )
                 {
                     unit.IsFirstPickUnit = false;
                     
                     var serializedObject = new UnityEditor.SerializedObject(unit);
                     var prop = serializedObject.FindProperty( "IsFirstPickUnit" );
                     prop.boolValue = false;
                     serializedObject.ApplyModifiedProperties();
                     serializedObject.SetIsDifferentCacheDirty();
                     serializedObject.Update();
                     
                     if ( !Application.isPlaying )
                         EditorSceneManager.MarkSceneDirty( unit.gameObject.scene );
                 }
 
             }

That didn't work either.

What am I doing wrong? It keeps leaving the flag as "true" on any object modified in another scene. (even if I hit save)