When OneDrive initializes and runs first setup for Backup of Desktop, Documents and Pictures directories, the current setup logic creates a duplicate Documents folder in %USERPROFILE%.
An additional step is required to prevent the duplicate directory, and verify that the symbolic link for %USERPROFILE%\Documents is pointing to %USERPROFILE%\OneDrive\Documents
OneDrive Backup setup runs
OneDrive creates Documents link in %USERPROFILE% (Two Documents directories now exist in Explorer)
OneDrive Backup starts moving %USERPROFILE%\Documents to %USERPROFILE%\OneDrive\Documents
%USERPROFILE%\Documents is now empty (Two Documents directories exist in Explorer)
If %USERPROFILE%\Documents is empty: check step 2
Paths need to be expanded. C:\Users\%USERNAME%\Documents
If C:\Users\%USERNAME%\Documents is empty, Delete C:\Users\%USERNAME%\Documents
Check C:\Users\%USERNAME%\OneDrive\Documents has created symbolic link to C:\Users\%USERNAME%\Documents
If this isn't done, applications writing to the absolute path of C:\Users\%USERNAME%\Documents will not be backed up, and users will have files go missing during an OS Update. The application will not write to C:\Users\%USERNAME%\OneDrive\Documents. It will use the absolute path.
While two directories exist, the symbolic link is bugged, and will not correctly redirect C:\Users\%USERNAME%\Documents to C:\Users\%USERNAME%\OneDrive\Documents
Please patch OneDrive setup to include these checks