I think they have solved your problem without you knowing it ;D
for icon markers use setmarkertype "empty"
for elliptical and rectangular markers use setmarkersize [0,0]
and that will make them dissappear, so if you want to change an elliptical marker to an icon marker, i would say have one of each at the same spot, and simply make them appear when you want the certain kind of marker
ex.:
you want an objective marker to turn into a rectangal marker (don't know why you would want that but its just an example
)
start with the objective marker there and the rectangle marker set at the size 0,0
when you want them to change, you set the objective marker to empty and set the size of the rectangle marker to whatever you want
in fact, this would be nearly impossible to notice even by opening up the mission in the editor, except that you have the script that changes it...