If you delete a struct in Windows Explorer manually, then open a project/BP, it will ask to delete and clean up the reference/variables it can not find. If you do this the BP will be broken and not compile. It will complain about the missing variable but it is not visible to delete.
Searching for the variable will display it but you still can not navigate to it.
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-89939 in the post.