The systems described herein are configured to enhance the efficiency of memory usage and access in a VM file system data store with respect to allocating memory in large and small file block clusters using affinity metadata and propagating and maintaining the affinity metadata in support of the described allocation. In order to maintain affinity metadata of the large file block cluster, affinity generation values stored on the large file block cluster are read and cached affinity generation values for each small file block cluster are read from an in-memory cache associated with the large file block cluster. When the stored affinity generation values and the cached affinity generation values do not match, affinity metadata from all the small file block clusters associated with the large file block cluster is used to update the affinity metadata of the large file block cluster and the associated cache.