lpr -r -s file no longer causes deletion of file from the queue. The reason for this is that the code that was responsible for this behavior has been disabled since it also made lpd vulnerable to exploit by a remote user who could cause any file on the print server to be deleted. This is probably the same case as the most recent CERT advisory on BSD line printing daemon. Unfortuantely, I wasted a day rediscovering this myself. :-( See bug 717 (which is now obsolete and should be cancelled) for details. That bug includes a patch to restore lpr -r -s functionality, but that patch re-introduces this security hole into lpd.
*** This bug has been marked as a duplicate of 717 ***