I have the same problem but it's easy to just restart the connection from 
nautilus and then save the file again from gedit and every thing would be fine, 
i agree that it's annoying but i never got the 0byte file problem, i just 
refresh from nautilus twice then the connection is back up.
And i don't think its a hard problem to fix either, just sending a 'NOOP' 
signal to the ftp server and let the user choose how often it would be sent 
shouldn't be that hard. ( that's just what i think, might be wrong though )
I add my vote for to the people who want this feature to be added.

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Nautilus does not handle FTP timeouts well
https://bugs.launchpad.net/bugs/410288
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