Utility and Notifier are independent apps so they don't share settings. Right-click the tray icon, go to Settings and point the first folder to DarqUI in your new game location.
EQII Wikia was migrated to fandom.com by the site owners, but their new site is not compatible with the in-game browser. Fandom has refused to support the older EQII browser, and unfortunately custom UI authors are not able to change it.
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