Method and system for automatically tracking packages in automated packaging system

A system of tracking product groups through an automated processing system, comprising:

• a sequencer which sequences a plurality of product groups, each with a corresponding accompanying physical position identifier, into the automated processing system according to a predefined ordered sequence;
• a transport system which conveys the sequenced plurality of product groups and accompanying physical position identifiers through the automated processing system;
• one or more scanners which scan the position identifiers of the plurality of product groups prior to exiting the automated processing system;
• one or more processors which review the scanned position identifiers to determine, based on the predefined order sequence and expected position identifiers of the sequenced plurality of product groups, if any of the sequenced position identifiers are missing, the one or more processors configured to associate each respective product group with its corresponding order if no sequenced position identifiers are determined to be missing, and if any expected position identifier is determined to be missing, to infer identification of the missing expected position identifier based on the predefined ordered sequence and received expected position identifiers, and to associate the inferred position identifier with its corresponding order.