If you install WordPress using the WordPress Toolkit will automatically appear in the WordPress Toolkit. You can easily add manually installed WordPress or detached WordPress websites from cPanel WP Toolkit.
Steps to add WordPress website again to cPanel WP Toolkit if it is detached.
Step 1. Log in to your cPanel account.
Step 2. Click on the WP Toolkit icon.
Step 3. Click on the "Scan" button.
Once the WordPress Toolkit completes the scanning, cPanel WP Toolkit will add your WordPress website back to its list of managed websites. You can then use the WP Toolkit to manage your website's plugins, themes, backups, and other settings.