Can I use Hong Kong Airport Express Travel Pass during the 3 day unlimited time?

No, as for Travel Pass itself, it contains one or two AE single journey(s) plus 3 consecutive days of unlimited travel on MTR (except AE, East Rail Line First Class, Lo Wu and Lok Ma Chau stations). But if you recharge the card, you can used it to take ferry, bus and tram. At the same time, you will enjoy some discounts. :-)