The look & feel resources (logo, favicon, and stylesheet) are stored in core.Documents. If you want to delete ALL custom favicons at both the site level and all projects, you could execute SQL like this:

    DELETE FROM core.Documents WHERE DocumentName = 'labkey-favicon.ico'

If you only want to delete the favicon at the site-level or on a specific project you'll need to add an appropriate condition on Container.

Note that these resources are cached aggressively, so you'll need to restart your server to see the changes. Similar queries should work for clearing logos (DocumentName = 'labkey-logo') and stylesheets (DocumentName = 'labkey-stylesheet.css'), if needed.

Adam