
I'm sorry you are facing this.
Can you tell us if you are in the US?
Tell us a bit more please - the flock you are hatching the chicks from is yours, but this is your job to hatch chicks. Are you supplying chicks to an individual or company for re-sale, for production, meat, etc.?
Your Landlord/Boss (?) I would assume has a say in the quality of chicks. If the chicks are for breeding, re-sale, production, etc. then likely a deformity would be an automatic cull, but it depends on business practices/guidelines.
A lot of folks may not agree - but personally, if the chicks are not thriving and they have deformities, then I would cull. Chickens that have deformities should not be used for breeding and they may later on have more developmental/production issues. That said, 12 chicks is a lot to cull, so ask your Boss/Landlord to help you make some decisions on that.
I absolutely understand culling very hard thing to do. I'll provide a couple of links that may help make the process a bit easier on you mentally. I do use a knife to cut the head off, but in one article a good sharp pair of scissors is used (the article is tastefully done). The other link provides information about how to make a quick and simple CO2 chamber - this is more hands off, but if you have multiple chicks that need to be culled, it would be easier on you and more humane for the chicks than drowning them.
Deformities can be caused by so many things. If you are using pullet eggs, this could be part of the problem. You mentioned a couple of times you were having 100% success rate until there was a snow storm a while back - this may give a clue as well. What happened during the snow storm - did you lose power, maybe the electrical circuit to the incubator was damaged? Humidity and temperature changed. I agree, re-calibrating the incubator is a good idea. Using eggs from parent stock that is mature, well feed and that has been given vitamins for a week before eggs are collected may also be helpful.
I'm not a breeder nor nutrition expert, but sitting down and comparing what has changed may get you back on track.
https://www.backyardchickens.com/ar...-for-squeamish-people-slightly-graphic.74734/https://www.backyardchickens.com/th...ping-block-or-kill-cone.1333246/post-21777555