If your range manual recommends it, you may leave the oven racks in for the cleaning cycle with this caveat: They may discolor, lose their shine, and become hard to slide in and out. Unfortunately, you learned this the hard way.
There may be hope: Try rubbing the racks with a soapy steel wool pad. Rinse and dry. Rub a few drops of olive oil on the edges for easier sliding.
In the future, it's probably better to take racks out before running the auto cleaning cycle and clean them by hand.