In the editor, after you change a ScriptableObject externally and the changes are imported, other ScriptableObjects will retain a destroyed reference to that object.

To reproduce:
1. Download attached project "LoadAssetAtPath.zip" and open in Unity
2. Run the menu command TEST/TEST LOAD ASSETS PATH
Note: This looks at the fields of TestObject and determines whether its references ReferenceA and ReferenceB point to destroyed references.
It prints out in Console several messages:

"TestObject is assigned and the reference is alive"
"TestObject.ReferenceA is assigned and the reference is alive"
"TestObject.ReferenceB is assigned and the reference is alive"

3. Open ReferencedObjectB directly in a text editor, change the value of IntegerField to some integer and save it
4. Go back to Unity and run the menu command TEST/TEST LOAD ASSETS PATH

Expected result: In Console it will print same messages as before
Actual result: In Console it will print these messages:

"TestObject is assigned and the reference is alive"
"TestObject.ReferenceA is assigned and the reference is alive"
"TestObject.ReferenceB is assigned but the reference is destroyed"

Note: If you reimport all files, then the problem goes away

Reproduced on Unity 5.5.3p2, 5.6.0p3 and 2017.1.0b2