When you integrate your account, Cliniq Apps will not recognise your archived patients and will not pull them out in your data.
But what about the ones you archive after the integration?
Well, if you don't want Cliniq Apps to send any communications to those that you have archived after integrating your system, all you need to do is:
Go to Settings->Privacy Settings
Select Archived Patients (and maybe Deleted Patients)
Enjoy growing your practice!