yea, i'm actually having the exact same problem with my last reference.
all my shadowing is done. 2/3 references done. all transcripts received.
i called 2 days ago and the guy at PTCAS said to go ahead and esubmit
when the ref finally does it it will just show as complete like the others.
and if he completely flakes out and doesn't do it you can delete him and add someone else.