Issue with site redirecting to wrong domains.

I created a new site for a domain under example.example.com (a subdomain as the primary domain, DNS was set up in Cloudflare to point to the server), I created a blank wordpress site and used the wp all in one migration tool to export/import the new site. Everything worked to an extent, now I can't flip the DNS to our servers until I have fixed any possible under lying issues from the migration but in order to do that I need access to the site, which cPanel isn't allowing due to possible SSL issues/conflictions. My problems start since I change the example.example.com to example.com (the original sites domain) and when I go to said site, it then redirects me back to the first domain it was originally created with in cPanel, which is quite stupid because there is no redirects in place at all. When I try go to the HTTPS varient of said domain, it takes me to a different site all together. In my localhost file, I have set it up with our serverip example.com so I can work it from my local machine, but its not getting anywhere. Any assistance would be brill, I have a support request opened, but thought I would probably get a faster response here :-)