if moisture repeatedly gets into the basement it will start to smell sour down there, just like mine does all summer, because i have no ventilation. i run my dehumidifier from may until september and i still can't stay in front of it. and i don't even get water down there! just mild dampness from new jersey clay. point being: rethink storing fabric there. if it's really the only space, get it into containers with ventilated tops, well off the floor. put some potpouri or lavender in the containers. keep something on hand to un-smell the basement when necessary.
smack that contractor. he should have warned you about water in basements. if you have windows try to keep them open. you might feel safer with bars or something. if you have a/c then run it. it takes moisture out of the air.
i hope you get ahead of this. dry everything as soon as possible, and get to the washing when you can. if it has to wait, it should wait dry. if you don't know what a fiber content is, or if something will bleed, use a color catcher or retayne. i always use retayne, but a lot of members here use the catchers. better safe than sorry. bad problem. sorry this happened to you.