How to properly duplicate website

@cameronl, Grav is a flat file CMS, so any way you can copy all files from one location to another is fine. Using zip, FTP, scp, etc., whatever fits best in your workflow.

When all of the site's config settings are located inside folder /user/config/, you're done.

However, just copying is not enough when using so called Environment configuration. This is automatically used by Admin, but can also be enabled manually.

Environment configuration allows you to use specific settings per domain. Think of dev, staging, production settings. For example, you might want to switch off asset pipelining in dev, but switch on in staging/production.

The domain related settings are kept in separate folders:

1. /system/config/ contains all available settings with defaults.
   These should never be touched.
2. /user/config/ contains user defined settings that override the settings found in location 1.
3. Settings for specific domains which override settings defined in location 2. and 1.
   • /user/env/domain1/config/ for configuration settings specific for domain "domain1"
   • /user/env/domain2/config/ for configuration settings specific for domain "domain2"

Note: Grav 1.6 uses location /user/domain/config/ while Grav 1.7 uses /user/env/domain/config/.

That means, that when a site is being cloned from "old-domain" into "new-domain", the /user/env/old-domain/ folder should be copied (or renamed) into /user/env/new-domain/, and adapted as required for the new domain.

When using Admin, saved config files will automatically be stored into a folder using the current domain's name. Admin will not automatically copy the settings for the old-domain into the folder of the new-domain.

Getting back to your issue:
This might be caused by the Environment configuration. In the new domain, Grav will fallback to /user/config/, which might still contain your old settings.