to update your site to current DotNetNuke (from DNN version 4.6.2 and above):

• make a backup of all files AND database
• copy web.config to backup.config
• place a dummy app_offline.htm file (valid html) with at least 1 k size into the root of your DNN folder
  this will prevent access to your site, while you are working on it
• unzip DNN install package to your web site location hierarchically, make sure, that existing files get overwritten
  This will not affect your custom files and database content, where your portal content is stored
• copy backup.config back to web.config
• remove app_offline.htm file
• call your site, and you will see the installer upgrading your database. Make sure, there are no errors reported
• access your portal. In Host :: Module Definitions, check for module upgrades, current versions are now listed in the installable modules section.

Be glad, that you succeeded and enjoy your portal.