Hi Vassilis, thank you for your reply!
I think that's for mainly the procedure to get the Typou B (and the permanent resident certificate). I already obtained both of them back in 2012. My status hasn't changed and I still live abroad. I was in fact able to renew my passport a few months ago.
My main concern is.. May I come to Greece and leave without any problems? (Meaning.. maybe when leaving, the immigration officer might stop me to do my military service)