Do not update or change the version of bootstrap used by Kentico. The /App_Themes/Default theme is specific to the Kentico Admin interface. If you want to change your site to use a different version of Bootstrap then do so.
Start by getting a site setup in Kentico. Next, create a CSS Stylesheet with the same code name as your site. For instance if your site's code name is MySite, ensure the code name of your stylesheet is MySite. Next, in the stylesheet, navigate to the "Themes" tab. This will create the directory in the file system at /App_Themes/MySite. In there you can add any images, fonts, etc you'd like.
Typically what I do is add another CSS Stylesheet and call it Bootstrap and copy the CSS from the version I want to use. Then I include that stylesheet in the MySite stylesheet like so {% CSS["Bootstrap"] |(identity)GlobalAdministrator%}. This will "inject" the css in the same stylesheet so place it where you want; top, middle, bottom, wherever. Lastly go back to your site and set the stylesheet to MySite for your site and it will automatically include it in your site.
There are alternative methods to this but this one is the simplest and fastest.