As I recall if you try to manually delete a member file which there should be one. something like members/0013487.cgi
Then you need to edit another file I believe it is memberlist.cgi.
So In your case you may find it the other way around.
You might have a member file but the member number is not in the member list.
both files are in the member folder.
But to upgrade to threads it should not be a issue. Even if it remains Rick could probably clean that out for you with a trouble ticket.