This is not a bug in the backup that prevents backup, the question was thet the backup was not removed correctly. This is not related to your problem.
Nope, seems all of those folders have been deleted by the upgrade script before it noticed the server was full.
I guess I have to reinstall the entire thing, I just had to ask if there were a way around.
If you dont have a backup of the ISPConfig database and the Root/ispconfig and /home/admispconfig folders, you will have to reinstall ISPConfig.