Embodiments extend using sparse Merkle trees for smart synchronization of S3 buckets by overcoming fixed size limitations through creating another Merkle tree when the fixed size limit of the first tree is exceeded, and creating yet another tree when the second tree is filled up, and so on as needed. The method maintains a super Merkle tree of trees, in which each tree can be synchronized separately by keeping a strict division to trees according to generation number. The generation is passed from a source site to a target site during replication operations. Syncing between two data sites is efficient as the super Merkle tree of the source is synced with the super Merkle tree of the target using the hashes on the nodes, as in normal Merkle tree sync operations.