The disclosed embodiments provide a system for updating an index structure of a graph database storing a graph. During operation, the system includes, in the index structure, a first compressed edge store containing a first compact representation of edges in the graph at a first virtual time and a first series of updates to the edges after the first virtual time. At a second virtual time, the system creates a second compact representation of the edges from the first compact representation and the first series of updates. The system then appends, to the second compact representation, a second series of updates to the edges after the second virtual time to produce a second compressed edge store. Finally, the system updates the index structure by atomically replacing, in the index structure, a reference to the first compressed edge store with a reference to the second compressed edge store.