What happens when you delete a folder that is synced to Ubuntu One is different from what happens when you format your hard drive.
If you delete a folder of a file, when Ubuntu One syncs, it notes what you you have done and does the same thing in the server. Then when you login to another device that is in sync with Ubuntu One, the same information is passed on to that device and the folder is deleted as well.
However, when you format a partition containing Ubuntu One installation and your synced data from a LiveCD or USB, the Ubuntu One client software gets erased and cannot run. Thus, the server doesn't know what has happened to your folder and won't delete it until you reinstall Ubuntu and Ubuntu One and login to your Ubuntu One account. At that point the server may treat your newly formatted computer to be a new computer and Ubuntu One will download all the synced folders and files.