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Those files are technically supposed to be hidden (typing ls will not list them, but ls -a will).
I don't know about hiding them, but you can make them unreadable by changing their permissions.
You can also run SFTP with the chroot(8) command, which will remove the parent directory of whatever directory you're in (making that the apparent root directory).
Other than that I would consult the SFTP documentation for the server you're using to see if you can "hide" files the way you want them.
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