Document folders created in the Content menu have a Can View and Can Edit tab which determines which roles can see each folder.
If a user does not have permission to view a document folder, they will not be able to select it when uploading a document to an employee.
To resolve this:
Go to Setup and click Content.
Click Documents, then select the document folder that the user cannot see.
Click Edit in the top right corner.
Click Can View and select each role that needs to see this folder.
For example, if the employee has he role HR System Owner, and you are sure that all employees with the HR System Owner role should see this folder, click this role so that it's highlighted in blue.
Click Save.
Click Can Edit and repeat the process above, then click Save.