Thanks for your response. I found out what happened, the hosts unzip package cleared out the existing directories before adding the compressed files. There was actually many more problems than I first relised. So I won't be using that anymore, instead I'll uncompress on my local machine and ftp the files up, replacing the existing files.
So that I don't further stuff this up any more, after having backed up everything including the database, should I remove all the current files and install a new site? Then once the modules are installed, reattach the new site to the old (existing) 4.8 database? Would this work? I'm assuming I would have to update the connection strings and machineKey in the new sites web.config to make this work?
What I have tried so far;
1. rolled back all file changes and start the site, this sort of works again however I am unable to log in anymore and the login module won't load.
2. rolled back all file changes (again), and uploaded the unzipped install package, this just didin't work (i think because the modules aren't installed). I also changed the release.config to web.config updating the connection strings and machineKey, but this still did not work, no modules would load.