Upgrades to be made without affecting employee data when this wasn't intended

Another point/request received from one of my account managed clients; Intertek: "We have had some instances recently where upgrades and removed data from payrolls/employees which has then affected the inclusions/exclusions in their salaries. This should never be the case so I will be requiring answers here as to exactly how this can happen." If this can be corrected/resolved with information I can go back to the client with?