Data storage system with automated correction of reference counts in addressing structure to avoid capacity leakage

A data storage system having storage processing circuitry and physical storage media, the storage processing circuitry executing computer program instructions to cause the data storage system to provide secondary data storage services to host computers including data deduplication functionality and reclamation functionality, the deduplication functionality including storage of unique data instances with associated reference counts each indicating a respective number of distinct references to the associated data instance, the reclamation functionality reclaiming storage for reuse based on reference counts of associated data instances reaching zero, the data storage services further including:

• performing one or more foreground processes in a manner that produces incorrect-high reference counts greater than corresponding numbers of actual references to associated data instances, the incorrect-high reference counts resulting in loss of storage capacity by non-reclamation of data instances when their number of actual references has reached zero and their reference counts are non-zero;
• and
• performing a background process of correcting the reference counts by, for each of the unique data instances, (1) copying the unique data instance to a new data instance with an initial reference count of zero and making the new data instance unavailable for reclaiming, (2) scanning a set of referencing structures for all references to the unique data instance, and for each reference (i) replacing the reference with a new reference to the new data instance, and (ii) incrementing the reference count of the new data instance, and (3) upon completing the scanning, making the new data instance available for eventual reclaiming based on its reference count reaching zero;
• wherein replacing the reference with the new reference includes replacing a pointer to data of the unique data instance with a new pointer to the same data in the new data instance as part of a garbage collecting background process;
• wherein each of the unique data instances includes a respective associated existing reference count resulting from the foreground processes, the existing reference count having a non-zero value, and wherein the copying of each the unique data instances to a respective new data instance refrains from copying the existing reference count and instead creates a new reference count with the initial reference count of zero, for use in the subsequent steps 2 (i) and 2 (ii) for the new data instance;
• and
• wherein making the new data instance unavailable for reclaiming includes setting an indication that indicates to a reclamation service that the new data instance is unavailable for reclaiming, including while the new data instance has the initial reference count of zero.