Your logo doesn't transfer into your QR codes from the branding tab. This actually works in your favor since it allows you to change the image in your QR code as often as you wish. If you want to highlight a presenting sponsor on your event page, but use your logo in your QR code, you can absolutely do that!
Remember, customizations to the dot shape, color, or logo for your static QR codes or dynamic QR code aren't preserved once you exit the customization screen. Be sure to download your QR code(s) once you're done customizing.
You might also be interested in these articles: