OK, here's what we have. Two different sites. Two different configuration.php files. Two different databases. Yet, somehow, you get the same changes applied to both sites. Now that we have ruled out all the reasonable, common issues we'll have to take a bold step into the "oh crap, this can't be
that" territory.
1. I see that you have a $live_site parameter in your configuration.php file, i.e.:
public $live_site = 'https://akeeba.xxxx.com.au';
Are you absolutely sure that the $live_site of each site (original and clone) is set to point to the respective site? Have you tried removing it?
2. Do you have a .htaccess file? Can you please try removing BOTH .htaccess files temporarily and see if making a change to the clone site now affects the original site?
3. Did you check the URL on your browser when making the changes? If you log in to your clone site but the URL you see in the browser's address bar is the main site's you have something that's doing a redirection upon login. Since you've checked the two items above (live_site and .htaccess) the only thing that remains is custom coding, a non-standard back-end / front-end login module or a system plugin which performs this kind of redirection. Since the problem started "suddenly" I would suggest tracking your steps back to when the problem started and think about anything you installed or changed to your site.
4. There is a very slim chance that your host is using a code cache. Code caches are completely transparent to you and the code running on your server. They read a PHP file once and they keep it in memory, in a parsed format, to speed up page load. This is terrible news if you are talking about configuration files since any changes made to them (e.g. when you finish the restoration process!) is not take into account unless the code cache expires. When that happens depends on the server configuration. The only way to know if you have such a code cache (e.g. APC, XCache, WinCache...) is asking your host.
5. Right into the "this can't really be happening" zone we can find more exotic reasons, such as having a different database user in both sites but actually using the same database. I don't buy this explanation but there's a simple way to find out. When restoring your site use a different database table prefix for the cloned site's database. Then look into both databases, the main site's and the cloned site's. You should see the tables with the new prefix in exactly one database. Which one is it? If it's the main site's database then this exotic reason is actually what happens.
6. Finally, I have seen some rare extensions with custom database drivers. It is possible that they do keep the connection information of the old database somewhere. Unfortunately I can't know which one and where it stores that information.
Nicholas K. Dionysopoulos
Lead Developer and Director
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