unix2dos is useful to convert file before transfering it to dos/windows machine. As you transfer it unix-to-unix, there's no need for it. Well, maybe you have it in dos format on the first unix already, however you edit/view it with tool that knows dos-format too, while after trasfering to the second unix, you edit/view it with tool that knows only unix format.
As last chance (if the file is really in dos format), to do the conversion, download file to windows using WinSCP in "binary" mode and upload id back in "text/ascii" mode. It should do the conversion for you.
Note that command line scp does not do any conversion of the file, so I doubt that it garbled the file.
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