I agree with the others ... I think it would be very difficult to do embroidery after a machine is quilted. Just too darned awkward to work with, let alone how you would tie in or knot off your threads.
The good thing is, that you are discussing this with your LAQ.
It could be that s/he is not comfortable with working with an embroidered quilt.
As FelineF suggested, perhaps she is talking about doing a panto where there would be no control, to avoid the embroidered areas. You've done far too much work in doing an AOTH, so it might be best to look around and find another LAQ'r that can do what needs to be done for you. Be sure to ask to see other similar work that has been done, to make sure that you are going to get what you want ... and not be disappointed, and heartbroken!