Reset N1 brain, plugged in N3 brain, now N3 looks like N1

[rlknight02]

Ok this may be a complicated question but I would appreciate some help on this please. I have an N1 headunit and BOTH the N1 and N3 brains. I had the N3 installed because I heard the ipod interface is much more advanced than the N1. I received a 40MT 1.1 disc in the mail because I had ordered it before I received the N3 brain. My N3 brain was already in my car today, so I unplugged that brain, plugged in the N1 to reset the brain using the instructions I found here because it had been upgraded and locked out. OK SO I plugged the N3 brain back in and it now seems (as if) it has also been reset because it looks the same as it did after I downgraded the N1 brain. My question is now that it seems as if I had downgraded the N3 brain with N1 software (or so it seems), did I ruin the ipod interface on the N3?? If so can I fix it by upgrading the N3 with a newer disc?? Or is it going to be just fine as far as the ipod goes, but only having N1 navigation software (which is all I know). I have not yet purchased an ipod but was going to get one this weekend so I cant test the interface yet, and I am also currently without an N3 disc. Please help! Thanks everyone!