According to certain aspects, a method can include receiving an indication that a restoration of a deduplication database using a secondary copy of a file associated with a secondary copy job is complete; retrieving a first data fingerprint from a data storage database, wherein the first data fingerprint is associated with the secondary copy job used to restore the deduplication database; retrieving a second data fingerprint from a deduplication database media agent, wherein the second data fingerprint is associated with the secondary copy job used to restore the deduplication database; comparing the first data fingerprint with the second data fingerprint to determine whether the first data fingerprint and the second data fingerprint match; and transmitting an instruction to the deduplication database media agent to rebuild the restored deduplication database in response to a determination that the first data fingerprint and the second data fingerprint do not match.