With the recent update of the Creative Cloud Desktop app (188.8.131.524) we unfortunately introduced a bug which causes the creation of a new Creative Cloud Files folder, and re-sync of all content. This will only occur the first time the sync application runs after the update. This has caused understandable pain and confusion, for which we truly apologise.
The Creative Cloud Files app contains logic that supports the use of multiple Adobe IDs. This allows you to sign out of one ID and in to another, but keeps your Creative Cloud content separate. When you sign out and change IDs, the app moves the previous Creative Cloud Files folder and it's contents and appends it with the previously signed in ID (User@AdobeID). It then creates a new main folder and starts to sync content of the new ID.
The bug which I mentioned previously occurs, as the app believes an ID switch has taken place and as such, moves the current Creative Cloud Files folder and tries to append the previously signed in ID. As no switch has actually taken place it manifests as (Unknown). The app then creates a new main folder at syncs down the data.
Essentially what you end up with is a Creative Cloud Files folder with your newly sync'd data and a Creative Cloud Files (Unknown) folder that contains duplicate data.
This occurs once, after the last update completes.
The fix is to simply delete the Creative Cloud Files (Unknown) folder.
I would advise that you ensure you have no pending edits that you may have made offline and that you check the contents of the new, main Creative Cloud Files folder contains everything you expect it to. If not, check the contents of the Creative Cloud Files (Unknown) folder.
If there is still a discrepancy with your data, you can check on creative.adobe.com to confirm your data is there.