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I was about to backup my archlinux, following this guide to my FritzBox, (which enforces a NTFS system that I mounted via samba) as I remembered, that NTFS is not capable to keep permissions and other stuff like symlinks.

There is also no encryption available which is really bad because it would break the idea to encrypt my laptop :) So I was wondering if there is a method which can do incremental backups like rsync but creates something like an encrypted tarball 'on the fly'?

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dar may be worth a look (tar replacement with encryption, per-file compression, incremental, catalog). But like tar it's rather a low level app, usually you write a script around it that handles the whens, whats, and hows... –  frostschutz Mar 27 '13 at 21:52

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I would mount ecryptfs on the ntfs filesystem and still use rsync - as long as you don't need to read the files from windows. Just watch out for long path names as you might hit some trouble:

As a side note, I haven't tried this but the encfs4win project looks good if you need access from windows as well:

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