1. A method for threshold based incremental Flashcopy (FC) backup of a redundant array of independent disks (RAID) protected array in a deduplication repository by a processor device in a computing environment, the method comprising: monitoring changes in a multi-RAID configuration to metadata of a source production volume in a source RAID since taking a most recent FC backup on the source production volume and storing incremental copies of the metadata on a target production volume in a target RAID; and creating the incremental FC backup of the metadata periodically or if the monitored changes exceed a change rate threshold.