They were storing the Cloak in Hermione's magic purse. Presumably it was in there the entire time they were in the Manor.
But he scarcely heard Hermione: he had pulled out his Invisibility
Cloak and was running it through his fingers, the cloth supple as
water, light as air. He had never seen anything to equal it in his
nearly seven years in the wizarding world.
As they had lost Perkins’s old tent on the night that the Snatchers caught them, Bill had lent them another one. It was now packed inside the beaded bag, which, Harry was impressed to
learn, Hermione had protected from the Snatchers by the simple
expedient of stuffing it down her sock.
Harry bent down and the goblin clambered on to his back, his hands
linked in front of Harry’s throat. He was not heavy, but Harry
disliked the feeling of the goblin and the surprising strength with
which he clung on. Hermione pulled the Invisibility Cloak out of the
beaded bag and threw it over them both.