Hello and welcome.
So sorry we didn't get back to you sooner.
Sounds like you are using macOS Sierra? If so, when you enable iCloud Drive, it moves all of your files from the Desktop and Documents folder to the iCloud Drive folder. Excellent that you have Time Machine setup and are backing up your data.
We greatly appreciate you taking the time to post that the issue was resolved and where the documents were located , in case others have a similar issue in the future.
We're here if you need us in the future,
C