Actually, it’s allowed to use 1 license for both production and dev sites if this is the same project. Anyway if you need to use another license for the production site you can deactivate theme in XStore > Dashboard http://prntscr.com/mlf6dw and then activate site using the new license you want to have for this site.
What version of theme do you use there? Try to update theme and XStore core plugin to the latest versions. We fixed issue with the deactivation in the latest updates. If you still have this problem just provide me temporary Dashboard access to the site where you want to deactivate theme and we’ll check.