What's most likely happening is that your FTP client and/or server are hiding any files that begin with "." (just like the HTTP server does in a directory listing, by default). In a pinch, I had to use Internet Explorer as my FTP client in the past and I had the same problem as you're having.
Not sure what the best solution is, other than a) try a different FTP client (or look for an option in your client to hide certain files), b) use your web host's online file manager tool (unless you've got a poor-quality host and they don't offer one), or c) contact your host to see what they suggest.
