According to certain aspects, a method can include receiving, in response to an indication that a data storage database is being restored to a second time before a first time such that the data storage database comprises a plurality of first archive file identifiers associated at the second time, a first instruction from a data storage computer, where the first instruction instructs a media agent to stop scheduled secondary storage operations associated with a deduplication database, and where the deduplication database comprises a plurality of second archive file identifiers; determining at least one second archive file identifier in the plurality of second archive file identifiers that does not correlate with any first archive identifier in the plurality of first archive file identifiers; and, for each of the at least one second archive identifier, instructing the deduplication database to prune an entry associated with the respective second archive file identifier.