The Q&A How to cleanly upgrade QGIS on Windows? outlines steps to upgrade QGIS. An important step recommended is "Make copy of plugins directory located here C:\Users\yourUserName\.qgis2\python\plugins and then delete the .qgis2 directory."
Are there not other elements besides the plugins folder to save for the new installation, that would otherwise be removed when uninstalling the version to be replaced? Is there a recommended process for storing such elements in protected locations outside of QGIS install folders?