I have always wondered about that but most probably Kate put the clothes in the wash at bath time so that rendered them useless.
Why was a second item needed for the sniffer dogs anyway? I think the simple answer to that is that there were so many dogs operating at the same time in different areas that they needed more than one scent source to take out with them.
Only three dogs were used to try to track the child. One patrol dog from Portemao who was given the blanket at 02.30am on 4th and two tracker dogs from Lisbon who were given the towel at 11.30pm on 4th.
The patrol dog wasn't used again and we don't know what the handler did with the blanket. He may have handed it back after his dog sniffed it. If someone had asked what time the photographs of G5A were taken that mystery may have been solved. All we know is that no-one was visible in or around the apartment at the time.
The tracker dogs were used again on 8th and 10th and the towel was used again because their handler had kept it in a plastic bag.
None of the other dogs sniffed anything because they weren't trying to track the child, their job was to find any lost or injured person.