Multiple key-value stores may be employed to smooth out random updates (based on the extent ID) to the EMAP database. The updates to the EMAP database occur in a two-stage manner: (i) using an append-only log store for the first stage and (ii) using an on-disk hash store for the second stage. The append-only log store is used to convert the random updates to sequential write operations on the EMAP database. Once full, the contents of the log store are sorted and moved to the on-disk hash store, which holds the updates for a transient period of time to enable batching of the updates. Once sufficient batching of the extent map entries are accumulated, those entries are sorted and moved to the EMAP database. Thereafter, the EMAP database can be scanned to find extent map entries having identical checksum bits to perform data deduplication.