I desperately began looking for the storage location of the AAM settings. I found very little information on google and thought that it would be good to post regarding this issue. Fortunately microsoft does have a KB article on the matter, but it was not easy to find.
So a little extra under the bonnet information when it comes to SharePoint. The AAM configuration does live in the Configuration Database, so why didn't it update on restore?
The answer lies with the WFE which also caches these values, Central Administration also displays the values from the cache and not the configuration database...In the event that they are out of sync you need to nuke the WFE by deleting the cache folders and allowing them to rebuild/refresh. Then your new settings will apply.
Also I found that whilst this was an issue I could not change the AAM settings, this is where I found the KB article.
The database stores only one XML string for each application containing the AAM configuration.
The following SQL queries will let you find the Alternate Access Mapping settings in the configuration database stored in the table dbo.Objects:
Where Properties like '<object type="Microsoft.SharePoint.Administration.SPAlternateUrlCollection%'