I recently ran into a problem of my web.config (in the "Views" folder) being replaced when I performed an install of uBlogsy. This removed some elements in that web.config that were added by MvcDonutCaching. It seems that the uBlogsy installer package comes with a web.config and just replaces the existing one entirely (it appears to be identical to the default web.config that comes with Umbraco).

This is not a good approach. If you need something in the web.config, you can using an XML transform file to transform the web.config and ensure whatever you need exists. If you don't need anything custom, then you may want to avoid touching the web.config entirely.