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Hello, Savin.
I developed DataFlash driver some time ago,(but it wasn't finished) and I had the same issue.
Simple solution is a ignoring of "unnecessary" bytes in DataFlash page. DF Page size is 528 bytes and if we will align that to 512 bytes we will losing 16 bytes per page only.
It can be used internally by DF driver for block regeneration(after 10.000 writes by Atmels's datasheet).
As for as I remember Atmels' proprietary filesystem - DFFS using this feature.
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