Flow filters are configured to both the non-Audiences and Audiences Klaviyo flows to ensure that if a customer is identified by both Klaviyo and Instant Audiences, that they only get sent emails from the non-Audiences flow.
This ensures that emails sent from Audiences flows are emails that would not have been sent otherwise, and Audiences flows do not send emails when standard flows would.
Setup guidelines for flow filters for each flow type can be found here.
If you need support with this please contact us.