@Nicram: The error message you got is related to the broken database on your server. It mappens when the server table is mising or incomplete. Regarding the websites, every website has to be created in a unique directory which is defined by the auto increment values, so directories can not be reused as this information is stored in the database version that you had before you restored the backup.
The ispconfig installer already checks the size of the database dump to try to prevent the problem. But it can not know how the exact size will be for your install, so we can check only that the database dump must have at least the size of all tables that are there for a new ispconfig install.
The release notes explian how to take a manual backup before you run the update, you should do this the next time before you update. But this is also not a 100% protection for broken databases as you might not see if your db is broken at that time.