The Content Acquisition System maintains a history of each acquisition (full or incremental) that runs against a data source. This history includes the Id of each record and information about all properties on each record. To determine the incremental change between acquisitions, CAS compares all the properties on a given record to determine if a record has changed between acquisitions.
If an acquisition does not find content that is listed in the history, CAS treats that content as deleted. That removal is part of the incremental change. Similarly, if an acquisition finds new content, CAS adds a record to the history. That addition is part of the incremental change.
This comparison can take a significant amount of time in large data sets.