1. A method in a computer system for performing retrieval and recovery of data chunks from alternate data stores within a storage management system, comprising: storing a data object containing one or more data chunks onto a plurality of storage pools within the storage management system, wherein the storage pools each comprise one of a deduplicating pool and a non-deduplicating pool; deduplicating the data chunks of the data object within one or more of the plurality of storage pools, wherein a single data deduplication information index, which contains an entry for each data chunk of the deduplicated data object, is stored on a storage management system-wide level; detecting a first inaccessible data chunk of the data object within a first storage pool within the plurality of storage pools; locating an undamaged and accessible copy of the first inaccessible data chunk in one or more alternate storage pools within the plurality of storage pools by referencing the entries for the undamaged and accessible copy in the system-wide deduplication index; retrieving the undamaged and accessible copy of the first inaccessible data chunk from the one or more alternate storage pools to the first storage pool; creating a new object holding the undamaged and accessible copy; cataloging the new data object within the deduplicating pool; assigning new identifiers to the undamaged and accessible copy; and linking the first inaccessible data chunk to the undamaged and accessible copy.