Do you know of a Windows-based FTP server that will receive files, but temporarily rename them as .tmp files during the upload. When complete, rename it to the original filename. This should ensure that the file cannot be accessed until the transfer is fully complete.
I am currently using FileZilla Server and I do not think it has this capability. I believe the feature I am looking for is similar to the "lock_upload_files" configuration for vsftpd.