The directories will remain at the FTP.
And the Resumes inside the directories, sub-directories will be processed and deleted from there. Once all the resumes are processed, The directory will be empty so that you can upload the other Resumes in the same directory, and those will process accordingly.
Also, If you want to delete all the directories, You can delete all other directories except the "SubUsersFolder" directory. The "SubUsersFolder" one is created for SubUser Bulk Parsing. And you can create a new directory as per your need.