Hi Bryan,
I think what you're doing is something that has not been forthought by the 3GPP / ETSI when specifying the SIM Cards. Of course I cannot speak for the designers, but based on my understanding:
Either you are
a) the phone. If "the phone" updates the card, then it knows by itself to re-read the state and/or reset the card physically after changing it,
or
b) the card (an applet on it). In this case, the proactive SIM refresh is used to tell the phone (which has no way of knowing otherwise to invalidate all its state about the SIM and start to re-read it
Of course I know that in todays "the phone" you have hundreds of software components on at least half a dozen of processors, so the old assumption that "the phone knows when it modifies" no longer holds true.
I am not aware of any method solving your problem, other than to write a small card applet which triggers the proactive refresh, after you send it a command via your channel...
Regards, Harald