See repro steps. The phantom references can be fixed by recompiling the child BP and saving it. Note that just loading ChildBP2 does not fix/remove the reference during compile-on-load, so it's a bit more of an issue than just 'bounce the editor after deleting an interface'.
Create InterfaceX with a function and an event
Have ParentBP implement InterfaceX, overriding a func from X
Create ChildBP1 inheriting from ParentBP
Create ChildBP2 inheriting from ParentBP
In ChildBP1, override a func from X
In ChildBP2, override a func from X
Save everything and close the editor.
Open the editor again and open ChildBP1 and ParentBP (but leave ChildBP2 unloaded).
Remove X from ParentBP, saying Yes to "would you like to transfer the interface functions to be part of your Blueprint"
Open reference viewer for InterfaceX
No references exist
References from both ChildBP1 and ChildBP2 exist
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-95398 in the post.