If we get a phone call from you guys, and then get an ACK back, we will carefully check the route you have given against the plogs and ammend as necessary (for fuel adjustment). Crew will always get an originally copy of your ACK anyway.
If we get a MAN followed almost straight away by an ACK, we won't give it a second look as we assume its something very minor.
Perhaps after its gone manual you could annotate on the ACK briefly what you have changed and save the phone call.