Chris,
Found it. Settings > Facilities was never filtering out deleted
facilities - it's a separate screen from your main Facilities list, with
its own database query, and that query never excluded deleted rows. Your
main Facilities screen already had this fix from a while back; this
particular settings panel just never got it.
Deleting a facility from the main screen was working correctly the whole
time - it just kept showing up in that one settings list because nothing
told that list to stop asking for it.
This is fixed in v4.2.7, published today. git pull and it is there.
Eric