EXTREMELY IMPORTANT: Please attach a ZIP file containing your Akeeba Backup log file in order for us to help you with any backup or restoration issue. If the file is over 10MiB, please upload it on your server and post a link to it.
Hands up, I'm an idiot. I fixed all my client sites with the JCE issue except my own. Face palm. I then dutifully went to Amazon S3, only to find no backups were there. Yay. Upon logging in I saw my S3 profile was set to no post processing. For the last few years. I have no idea how. The good news is, my daily CRON has been running, and I did indeed have all the backups. The bad news is I had nuked my site files and folders because I wanted a fresh install not an install over the top. Fortunately there were all in my cPanel's .trash folder. Yay. I'm saved. I copied them all to my root so I could start working out which one was far enough back not to be hacked. I restored a backup using kickstart, clicked "clean up files" and it wiped all the old backups. But the restoration was still a hacked website. DOH. I needed to go back further. And now the backups are not in trash. So I guess my point is, often for a hacked website we often don't know which version to restore, it's a bit of trial and error. Is there a way to clean up all files except backups? That would be useful in times like this. I know my ADHD ass clicks too fast and this is totally my fault, but I think this might be a use case for this feature.