Hello,
Oh, unfortunately, it’s known issue of the WooCommerce plugin. We have reported about this https://wordpress.org/support/topic/uploading-of-the-logo-in-the-personalize-my-store-section-reset-theme-options/ and also a number of other users https://wordpress.org/support/topic/woocommerce-shop-deleted-my-theme-customizations/ and https://wordpress.org/support/topic/woocommerce-setup-destroyed-my-layout/ We can do nothing from our side with this. If you don’t have DB backup before the setup wizard you don’t have options to restore settings.
Regards
