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mandib99,
Sorry to hear about your computer troubles. Hopefully we can help you figure out what is going on with your backed up data and get everything fixed.
First to your backup question: every time N360 begins a backup, it starts by scanning your system for new files that fall under the catagory or catagories that you have selected (stuff like Documents, Pictures, Favorites). If you have a set of files that fall under a selected category, they will be backed up no matter where they are on your computer as long as they are visible to N360. If you had created a special rule to back up a particular folder, and then moved that folder to another place, that would most likely not be backed up in the new location. It sounds, from your description, as though it is the former and not the latter.
One thing you should be aware of with regards to a restore - if your computer was reset to it's factory defaults, it may be that your data is backed up under a "different" computer. Each copy of N360 allows you to back up a total of 3 separate computers. When your computer was reset it may have considered the fresh install a different computer. In order to access those files, click on "restore," and then at the top of the screen select "change" in the restore from box.
If you would like me to look into the specifics of what is backed up on your account, feel free to send me a PM on these forums or an email (address in profile) I would be happy to pull up your account and let you know what we've got. If the backups were able to complete successfully then we should have no trouble restoring all of your data.
~scott