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How does Windows Server backup work?

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I would like to know how Windows server backup knows what files to backup.

I have 2 NAS boxes that I swap daily for offsite backup, from looking at the backup completion I can see Windows backup decides only certain files have been updated and sends them to backup causing Incremental backup as opposed to full. I also noticed this happened in 9 mins, this doesn't lead me to believe that a full comparison has occurred within the file system. 

Does this mean both my NAS boxes are out of sync?

Does Windows backup use a flag to indicate what has been backed up? - therefore missing it from the next day (swapped NAS box.)

Any information would be appriciated.


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