Despite what he'd said before, having Septimus along for the ride would make this that slight bit more bearable for Will. When the crew broke up, Will went to the castle. He had to explain his disappearance.
Approaching the throne room, he's notified by a guard that the Queen is on break, and that she and Sir Bannikur were off somewhere.
That was all the information he needed to know he wouldn't be seeing the queen before he left.
Returning to his office, he writes a short note to her, explaining the situation and how the two of them would be leaving for some time. He mentioned her dream, and suggested this may be what it was about. Sealing it with wax and the symbol on his ring, he has one of the guards hold it for her to read later.