Data is only collected for patients who are "active" in your clinical system. Data for patients who are deceased or have been made inactive/archived is not collected unless it is required for reporting and the practice has specifically enabled this option (available for MD/BP only and done by default for Communicare and MMEx users).
Therefore, when you are analysing your data using CAT4 you are only working with patients who are currently marked as active in your clinical system. If you find patients in CAT4 that you know are no longer active at your practice, you simply need to update them to be inactive in your clinical system; such patients will then be excluded from future data collections.