Killing Zryachiy and its consequences [Discussion]

I'm planning to eventually get all the achievements and one of them is "Eliminate every Boss once while playing as a PMC". I'm assuming that the 13th that im missing is Zryachiy but I'm deep into Lighkeeper's missions (currently Payback) and I wouldn't want to go through the pain of encoding the transmitter again after killing him. I've read somewhere that if you don't bring the transmitter into raid it will not decode if you kill him. Is that still the case? Also as a side question: do you need to have the transmitter in your hands to go through the bridge or is it enough to have it in your special slot?