I wasn't sure what time they were meeting- it seemed like it was a short time after retrieving Harry from lunch, but I couldn't find any specifics. Even if it was after three, though, they could (for example) send a Patronus to Flitwick asking where he was at three o'clock, but not to tell them anything else but that; and have Harry come there at nine, tell him to tell Flitwick not to report his arrival to anyone before nine, then Time-Turn in front of them.