I have a backup that involves mounting an s3ql file system and using  
'rsync --delete ...' to do the backup.

If a large folder (or file) is moved, there is a risk that the files will 
be 'deleted' before they area created again, possibly resulting in remote 
data being deleted then recreated.

Is this concern genuine?

Would doing: 'rsync' (with no --delete) followed by 'rsync --delete ...' be 
the best way to alleviate the risk of wasted bandwidth (and time) here? Or 
should I consider a snapshot, the 'rsync --delete' then delete the snapshot?

Any advice appreciated!

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