Did you candle them during lockdown to determine they were still moving? If so, the opening of the incubator would most likely be your problem. The pipped eggs that died were probably the result of lost humidity when opening the bator. Also, if you did candle them on the last days, when you move them around this confuses the chick inside which is already orientated to start his escape. This repositioning can be deadly if the chick cannot readjust and find the air sac. (This also happens from hatched chicks rolling eggs around).
I always try to get my humidity up to 90% + on lockdown and never open from day 18-21 (unless emergency). That's me though. Everyone is a little different and geographical location affects hatching styles too. Also, as chicks start hatching and drying the humidity will drop.
From my experiences, these are my educated guesses. I've had 4 incubators running non-stop for over 2 years now and everytime I think I've got it figured out, I get another curve ball, lol. I hope I helped and Good Luck!
