I don’t think changing favicon is EE only (although I may be wrong). Have you checked the html source in your page to ensure the links are pointing at your new images?
I don’t think it would be an enterprise issue as per : https://github.com/mattermost/docs/issues/1006
That references a directory called “static/files” and a file name that looks generated on the fly. I can’t see that file structure in my /opt/mattermost directories.
I have nginx out front and am a bit confused on exactly where the webroot is.
The file would be located under /opt/mattermost/client/static/files. Its filename is generated when the web app is built so it’ll likely change whenever you update Mattermost.