"Archived" email are the messages that have the inbox label removed. Gmail doesn't have folders. All messages hove 0 to many labels.
An email with the label "labelx" can be found under the "all Mail" label, or the "labelx" label. If it hasn't been archived it can also be found under the "inbox" label.
I have found that hitting the archive button without first attaching a label is counter-productive. this means the message only exists under the "all mail" label. For this purpose I have created a hide label. These are emails that I don't expect to ever need to read again, and someday if I ever come close to the gmail limits I might delete them.
If you want to find this rogue email you will have to use the search tools.