We needed 2 ways to connect to sharepoint. One via direct ip and another with username and password authentication.
We created an additional web site and copied the site settings of sharepoint and set it up with authentication and then found we had broken sharepoint.
We then deleted the new website in IIS and found that sharepoint just wants to come up with errors.
We tried to backup the site and create a whole new server to then restore to but this did not work. A user that had a page left open to the sharepoint site could still browse the site but it seems the entry point into the site is not working.
It might be something as simple as accessing it via the new IIS site has caused it to make some changes so it effectively has a dns issue.
I look forward to working with anyone that can fix this.