A method of prioritizing data for recovery in a distributed storage system includes, for each stripe of a file having chunks, determining whether the stripe comprises high-availability chunks or low-availability chunks and determining an effective redundancy value for each stripe. The effective redundancy value is based on the chunks and any system domains associated with the corresponding stripe. The distributed storage system has a system hierarchy including system domains. Chunks of a stripe associated with a system domain in an active state are accessible, whereas chunks of a stripe associated with a system domain in an inactive state are inaccessible. The method also includes reconstructing substantially immediately inaccessible, high-availability chunks having an effective redundancy value less than a threshold effective redundancy value and reconstructing the inaccessible low-availability and other inaccessible high-availability chunks, after a threshold period of time.