I was able to recover the logo in that position by editing the XML from Customize: HTML Editor: Show Logo.
I inserted some external image src into the empty quotes. This filled the space with the external image and allowed the "change" link to be available again.
After that I was able to upload a PNG of the company logo by the normal method.
Upon checking the code in the Show Logo template, the line is now:
<img src="/website/image?max_height=768&field=datas&model=ir.attachment&id=24&max_width=1024"/>
I can't find the logic that alters the template resulting in it going blank, but line 166 of odoo / addons / website / views / website_templates.xml is the line affected.
This is resolved for me, but will happen to someone again if the logic isn't changed.
So far I have tried to find the section in the HTML where it would have been and there is nothing there. I also set the company logo in Settings: Companies: CompanyName. This updates the logo for the "backend" but not the website. Is there a place in the backend where the logo for the website header can be set? Can I access the DB directly when using the odoo hosted SAAS?