1. An apparatus, comprising: a processor; and a memory containing logic operative on the processor to cause the processor to perform a process comprising: loading a subspace index comprising less than all index entries of a signature index service from a secondary media into a primary memory, wherein the loaded subspace index corresponds to a set of subspaces individually containing a set of signatures each corresponding to a data chunk stored in a data store, two of the subspaces having at least one signature representative of one subspace generally matching at least one signature representative of the other subspace; and reconciling the two subspaces associated with the loaded subspace index to remove at least one duplicate chunk by: using a resemblance metric to compare a signature of a data chunk in one of the two subspaces to multiple signatures of data chunks in the other of the two subspaces; and in response to determining that the signature of the data chunk in one of the two subspaces matches another signature in the other of the two subspaces, marking a data chunk corresponding to the signature or the another signature for deletion from a corresponding data store.