To confirm, the favicon.ico, was it replaced with yours in "..\Program Files\Qlik\Sense\Client" directory? Was the old one just renamed or was it copied and moved to another location (ie. did you delete the old one from the folder)?
For the title of each page, did you update both HTML files: client.html, hub.html in the "..\Program Files\Qlik\Sense\Client" folder?
HTML tag to change is <title>.
I copied over the existing favicon.ico file in the Client subdirectory.
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I have tested in 3.0 and it partially works for me (see image). Google Chrome is OK but Internet Explorer is only partially OK.
Using Google Chrome it works just as it should:
Using Internet Explorer the Title is updated but the favicon is the IE favicon
Caching may cause lots of problems and pains. I updated the favicon.ico, hub.html and client.html files before opening the Hub for the first time. I recommend that you install Qlik Sense, then change everything that needs to be rebranded before opening the Hub (or QMC for that matter) the first time. Just clearing the browser history has not worked for me in general.
You may run into access problems when saving the content in the C:\Program Files\Qlik\Sense\Client folder.