Wix Lightboxes are not connected to the Wix Stores app, you don’t have the lightbox showing in the site structure as you haven’t added any to your website to have one shown.
https://support.wix.com/en/article/about-lightboxes
https://support.wix.com/en/article/adding-a-pop-up
As your issue is to do with the editor itself and is not code related, for which this forum is to be used for, then you are better suited going through Wix Support for any more help with this issue.
https://support.wix.com/en/about-wix/contacting-wix-support