I did try to check-in the file via Workbench prior to creating the sub-directory in Aministrator. This is the error I received . . . 

E03060096: "Error accessing the path: <folder name>. Either the path does not exist or access to the path is denied." 
Plug-in Provider: CA 
Plug-in Name: CA Harvest SCM Workbench 
Plug-in ID: com.ca.harvest.workbench 
Version: 13.0.0.28 
The error was detected in Class: com.ca.cmsdk.process.CheckinProcess.

CA Harvest SCM all versions and platforms

In her "To" field she had specified a folder that did not previously exist. We changed the "To" field to a folder that did exist in the SCM repository, and then made the corresponding change to the "From" folder. Harvest was able to create the missing folder at that point and check in the file.