Whoops... forgot that ldapdelete just takes a list of DNs, not an LDIF file. See the manpage.
You could remove the "dn::" part, base64-decode the DN and put that on a separate line. Or you could use ldapmodify instead, with input
dn:: Y249w5x6ZW1lbHRldMO1IEJyaWfDoWQsY249ZGFuaWVsbCxjbj1hZGRyZXNzYm9va3MsZGM9ZWNlbnRydW0sZGM9aHU=" changetype: delete