Thanks for reaching out to us. It sounds like you are using a special FTP program/script that is handling the uploads in an unusual way (possibly deleting files internally and failing to upload the newest version?). Unfortunately we are limited with the support we can provide to customers using these types of custom FTP methods. If you use a generic FTP client like FileZilla, you should be able to see that there is no problem with upload.
Please send an email to email@example.com if you would like to discuss different ways of setting up your use case via FTP.