A perfect hash vector (PHVEC) is created to track segments in a deduplication file system. Files are represented by segment trees having hierarchical segment levels. Containers store the segments and fingerprints of segments. Upper-level segments are traversed to identify a first set of fingerprints of each level. These fingerprints correspond to segments that should be present. The first set of fingerprints are hashed and bits are set in the PHVEC corresponding to positions from the hashing. The containers are read to identify a second set of fingerprints. These fingerprints correspond to segments that are present. The second set of fingerprints are hashed and bits are cleared in the PHVEC corresponding to positions from the hashing. If a bit was set and not cleared, a determination is that there is at least one segment missing. If all bits set were also cleared, a determination is that no segments are missing.