In Atlas Mugged, if you choose to go to Hollow Point, you will go to Old Haven with Fiona and Sasha. Here, you can talk to the girls and ask Fiona to give you back your shoe. And she gives it back to you. From now on you wear both of your shoes. Look carefully to Rhys' feet when he activates the Atlas portal to get the Gortys. He still has one shoe missing. Nice sock anyway.
In Atlas Mugged Episode in the intro when Fiona lets go of Rhys, her hat falls off her head and into the desert and is clearly pointed out, but in the next scene with Fiona and Sasha her hat is back on her head again.