When new files are uploaded to an FTP server then the FTP server will set the default permissions for a file (typically it's 644, meaning read & write for owner, read for group and read for others/users). This is a configuration setting on the FTP server.
If you want to retain the file permissions (when replacing existing files) you need to switch off the safe-copy option: modify your profile, go to Copy/Delete settings page and switch off the option Make safe copies.