In case I'm not explaining this right, let me try a different way.
I open my Iphone native mail app. There is an email with an .ics file. I click on it, takes me to the IPhone calendar app, and I add the event. Call that Appt "A".
I then open the IPhone calendar app. Appt A is there. I then add a second appt for later in the day by hitting the + key . Call that Appt "B". So now, when I open my IPhone calendar app, both Appt A and Appt B are there. But if I go to my desktop calendar client, or to my IPad, Appt B is there, BUT APPT A (the one created by using the .ics file) IS NOT!.
If I go through the same sequence on my IPad, both Appt A and Appt B end up on my desktop, IPad, and IPhone! So everything works perfectly and as it should EXCEPT that the appt CREATED on my IPhone using the .ics file never leaves the IPhone to Exchange.
And again, if I create Appt A with the .ics file on my IPad, once it appears on my IPhone (and it does), and if I delete it on my IPhone, it deletes on my IPad and my desktop. The only thing that does not work is that an appointment created on my IPhone does not register to my Exchange account if the entry was created on my IPhone using an .ics file.
If I did not have the IPhone mail and calendar set up properly on the phone, Appt B would not propagate across all devices when I add it to my IPhone manually. Nor would deletion of Appt A on my IPhone (If I created it on my IPad or desktop using the same .ics file) delete the appt from my other devices. But it does!