I just tested it.
Created a directory called "test" with a file in it. => upload
==> Remote Folder and File are created
Renamed the local directory to "Test" => Refresh
==> Remote Explorer shows "Test" als new to upload (but not "test" to delete)
I then "upload" the "Test" folder
==> RE is uploading folder and File.
==> If I click "Refresh" again, the folder is still showing as new.
Looking on the ftp server, the new folder "Test" was created including the file, but the old folder "test" is still there also.