Notes is doing this when the email his from an r5 client and using the Form “Personal Stationery”. The form contains a field called “$NoPurge” and this field is responsible to keep the important document that should not be deleted. The value of this field his blank so the archive agent skip the deletion of this message. Usually there is a date there, and if the date is in the past the deletion is authorized, if the date is in the futur then the deletion is rejected.
Create an agent to delete this field and you will then be able to archive the document without any error messages.