When I flew my cat over, I had her blanket and an old tshirt of mine that was always in her crate when I took her to the vet. When I got to the airport, they made me remove the blanket and the tshirt. I also had food and frozen water in the bowls, which they made me remove.
I was told all that was allowed in the crate was a wee wee pad. They fed and watered her in the airport, but removed it before the flight. So make sure you check with your airline.
As soon as she landed and got to the ARC, she was removed from her crate and given food and water. The person at manchester pets on jets assured us that no harm is done by keeping the food and water from them during flight, and actually is better so our furry family has less chance to get sick.
Good Luck!!!