Late cancel is now issued to reservations cancelled after the cancellation window closes instead of a cancellation number(possibly immediately after booking for non refundable stays). The point of a cancellation number is to be able to prove you cancelled within the window in the event of a no show charge.

Someone must have canceled it, whether it was the the hotel or HH due to thinking it was a duplicate, or someone called to cancel, or they pulled up the wrong confirmation and cancelled is anyone's guess. Sometimes technology does weird things and no one really knows why.

Glad the manager reinstated it for you as they should. Hope it worked out.