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Assume I've cloned PROD database to TEST with RMAN "duplicate target database to CLONE from active database;". After several days I need to refresh CLONE. Will RMAN transfer all the datafiles from PROD to CLONE or only datafiles with changed data if I will issue "duplicate from active database again" ?

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It will transfer all datafiles again.

The previous duplicate already changed all your datafiles. You have a new database incarnation, with a new name, a new dbid, which was written in the datafile headers.

RMAN duplicate skips existing datafiles in case of re-running a failed duplicate so it does not perform the same work again, but that is a different use case.

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