One embodiment provides a system which facilitates organization of data. During operation, the system identifies an original data chunk stored in a non-volatile memory of a storage device, wherein the original data chunk is a logical chunk which includes original logical block addresses. The system stores a first mapping of the original logical block addresses to original physical block addresses in a first data structure. The system assigns new logical block addresses to be included in a new data chunk. The system creates, in a second data structure based on an order of the assigned new logical block addresses, a mapping of the new logical block addresses to valid original logical block addresses. The system stores, based on the first data structure and the second data structure, a second mapping of the new logical block addresses to the original physical block addresses.