What happens during the T3 blank template update?

I followed the tutorial to create my own style.

1. Now this folder templates\t3_blank\css\themes\mystyle\ contains bootstrap-responsive.css and others. Do I have to update these manually now or does the update take care of these non custom files?

2. my favicon gets overridden on updates, is this a bug?

3. in templates\t3_blank\tpls\blocks\ I customized the header.php and head.php but these customizations are lost as well. how can I customize the template so it does not get overridden but still updated?

cheers