An information management system can manage the removal of data block entries in a deduplicated data store using working copies of the data block entries residing in a local data store of a secondary storage computing device. The system can use the working copies to identify data blocks for removal. Once the deduplication database is updated with the changes to the working copies (e.g., using a transaction based update scheme), the system can query the deduplication database for the database entries identified for removal. Once identified, the system can remove the database entries identified for pruning and/or the corresponding deduplication data blocks from secondary storage.