Well not entirely, If you had FlashFXP set to overwrite existing files, it would reconnect and overwrite the file and you wouldn't get anywhere. In your case that only works because you have it set to skip the file if equal.
Connection lost: Site
Attempting to Reconnect.
Connecting to Site
That's the FTP server disconnecting/loosing connection.
Does the ftp server have a very low idle timeout?
Does it happen every single time? Would it be possible for me to access the ftp server and see if I can reproduce it?
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