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The de-duplication in this case is achieved by hardlinks of unchanged files between snapshots. This means, deduplication is only on file level, so even an append makes a new copy.

I've been looking for an rsync-based tool with encryption, but really couldn't find any. There is that uses rsync way of finding differences & keeps change log, but this is in fact normal full-snapshot & incremental backups: http://duplicity.nongnu.org/

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My understanding of what people looking for de-dup want is for their backup store to contain zero files with identical contents. With rsnapshot, if you rename a file, rename a parent directory of it, or move the file to another directory, you will get another copy of that file in your backup.

I've used rsnapshot for about ten years, mainly to make remote backups of data on SMB/AFP file servers, and something I had to actively discourage was staff using the moving of files/folders between higher level folders as a method of project management. One group in particular does video production so a project between yesterday and today might have only a change of a few bytes but because the project's folder was moved to a different parent folder (e.g. Completed/), rsnapshot would make a new complete backup of that project which could be tens of gigs. Filesystem snapshots like ZFS's avoid this problem but I haven't worked with how those are copied remotely.

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