I did redact the domain name, did not want it plastered about as I am sure after 13th Feb this topic might get a few clicks! 
I have now fixed it by renaming the 000-default.conf file and the --dry-run succeeded. Hopefully, deleting the file will not cause any more issues down the road.
It is odd that it has never caused an issue in the past.
Thank you @_az so much for your help, I would not have been able to figure this out without your help.