A method for managing deduplication reference data may include (1) identifying multiple of data containers configured to store a plurality of deduplicated data segments that are referenced by multiple data objects within a deduplicated data system, (2) maintaining multiple reference databases including (i) a first reference database corresponding to a first subset of the data containers and (ii) a second reference database corresponding to a second subset of the data containers, the second subset differing from the first subset, (3) determining that a data object references at least one segment within a first data container within the first subset but does not reference any data segment within a second data container within the second subset and (4) updating the first reference database with information specifying that the data object references at least one data segment within at least one data container within the first subset of data containers.