Of course. When you upgrade you are overwriting all code files with the new ones. If you have any customizations it's recommended that you backup the customizations and re-apply them post-upgrade. The code changed a lot from 1.10.x to 1.15.x so the customizations might need some updating if they don't work right away.
As for the Favicon, you will need to customize the code to accomplish this. You can run a grep for
favicon to find where it's referenced.