When an application is scanned there are notifications sent for any new policy violations. When the same application Id is used to scan a different application where these policy violations are not present, those violations are cleared. If the first application is then scanned again, the policy violations will be treated as new and notifications will be sent.
This behavior will also be observed if the same application Id is used to scan different branches of the same application with different policy violations.
Using the same application Id for multiple applications is not recommended.