Physical storage is replaced online in a data integrity storage system comprising RAID groups of physical disks in separate enclosures (shelves). All disks of a RAID group are located on a corresponding shelf, and each shelf is mapped by an internal file system to a separate independent logical address space partitioned into a plurality of blocks forming a blockset containing data and metadata. Source shelf disk data is moved online to disks of a target shelf using invulnerable data movement that ensures the integrity of the data, and source shelf blockset metadata is migrated to a corresponding target shelf blockset. After verifying the correctness of the target data and metadata, the source shelf and blockset are removed.