Mythconverg's channel table has a presumably recent column called 'deleted'.
Normally this field is NULL but if it has been deleted the channel entry isn't removed but 'deleted' is filled with a timestamp of it's deletion.
When running shepherd --configure it tries to get you to match a deleted channel to an XMLTV entry. Perhaps check this column for NULL and ignore trying to match it if it's populated with a timestamp.
If I manually remove the 'deleted' channels Antares SQL they don't show up in --configure of course.