1. A method of maintaining a signature repository in a data storage system, the method comprising: tracking storage of a plurality of data units in a primary storage subsystem, the plurality of data units stored in a native format corresponding to one or more source applications, the primary storage subsystem in communication with a secondary storage subsystem that is separate from the primary storage subsystem and is configured to maintain secondary copies of at least some of the plurality of data units, the secondary copies stored in the secondary storage subsystem in a non-native format; generating, by a signature agent executing on one or more processors signatures corresponding to the plurality of data units in the primary storage subsystem during a copy operation to the secondary storage subsystem; maintaining a secondary storage signature repository in the secondary storage subsystem and a primary storage signature repository in the primary storage subsystem, wherein the secondary storage signature repository comprises signature blocks for one or more unique signatures associated with data units in the secondary storage subsystem; wherein the primary storage signature repository in the primary storage subsystem comprises signature blocks for one or more unique signatures of the generated signatures associated with data units in the primary storage subsystem, where the signature blocks in the primary storage signature repository comprise: the unique signature; and one or more data unit entries, each entry corresponding to at least one of the of the plurality of data units in the primary storage subsystem associated with the unique signature; and wherein when a first data unit stored in a first location in the primary storage subsystem has the same unique signature as a second data unit stored in a second location in the primary storage subsystem, modifying the associated signature block in the primary storage signature repository to comprise: a first data unit entry that identifies the first storage location in the primary storage subsystem, and a second data unit entry that identifies the second storage location in the primary storage subsystem.