To me it appears to be a chemical poisoning from the excessive use of bleach and chlorhexidine. The heat lamps will cause toxic fumes.
I would stop the excessive cleaning with chlorix etc. as it can result toxic for the chicks.
Use apple cider vinegar instead and just simple old towels or bedsheets for the first week, then change to soft wood chips and sand.
Very sorry you lost so many.
Maybe try and leave the next clutch of chicks with their mother. The ones that will survive shall be very resilient.