I’ve done nothing but try to change the logo so far, so it’s fresh out of the Site Library.
Under Appearance – > elements, there is only one element listed and that’s “Home Merge”.
I’ve just switched over to GPP and this is all new. Sorry for the newbie questions 🤣.
The rest of the pages on your site is using the logo on Appearance > Customize > Site Identity. You can try deleting the default and add your own and see if it works. 😀
If it doesn’t try disabling some plugins and let us know how it goes. 🙂