Yes, you can sell your NFTs even after using them. The value of your NFTs does not decrease with the amount of usage. 

In case of Genesis Commander NFTs, you can continue using the heroes you’ve generated from them, even after selling the NFTs, as long as the Hero durability lasts.

Think of it like this: You had a chicken that laid eggs. You can sell the chicken, but you still have the eggs to make an omelette. 😉