What an update never touches An update replaces the product's own files. It leaves your settings, uploads, rules and add-ons alone.
Hooks: react to events without editing WBAMS A hook is your function that WBAMS calls when something happens. Hooks are the kind of customization an update never overwrites.
Will an update overwrite my changes? Not your settings, uploads, .htaccess or add-ons: an update never touches settings.php, the root .htaccess, storage/, your media uploads, and never removes an add-on. It does replace the theme files it ships, so customize a copy of the theme.