I don't think that your recruiter could actually change anything on your application without you signing a new copy - legally, you've gotta sign what gets sent in. Unless you signed a new application with the I/W designator instead of the AMDO one (the first page, at least), you didn't actually change what you were applying for, to the best of my knowledge. Something similar happened to me, which we caught before the package got sent in. I had to resign and resubmit that first page with the updated info on it.
Not sure about what to do in your situation at this point, though. Sorry for the lack of helpful advice there, other than just ask your recruiter again. Maybe they can call down to CNRC and get your application pulled before it gets considered, and resubmit for the next board? Just thinking out loud, as it were, I dunno if that'd be possible.
Edit: Well, if you already didn't get picked up for AMDO, it's probably too late to see if your recruiter can pull your package. I guess just wait and see - if you don't get picked up for anything else, you can always reapply with IW on there.