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Deduplication results inevitably in data fragmentation, because logically continuous data is scattered across many disk locations. In this work we focus on fragmentation caused by duplicates from previous backups of the same backup set, since such duplicates are very common due to repeated full backups containing a lot of unchanged data. For systems with in-line dedup which detects duplicates during writing and avoids storing them, such fragmentation causes data from the latest backup being scattered across older backups. As a result, the time of restore from the latest backup can be significantly increased, sometimes more than doubled.
Kaczmarczyk et al. (Mon,) studied this question.