Nested WP website

I have made a store for my website. As I had problems with woocommerce in the past, I installed that in a seperate directory on my main website. I hoped this was okay for the liscence, but now I see if I activate the liscence for the new store, then liscence for the main website is deactivated... Is there now way to have the liscence work for both WP installations? It *is* the same website... Thanks!