Chicks from my own eggs are consistently dying at hatch

That is a good idea, to see if the problem is the same across all hens or if it is only specific ones.

Although the food coloring idea doesn't always work as well as it sounds. I've tried it and gotten colored eggs, but I've also tried it and gotten non-colored eggs, even though I thought I did it the same way each time. I've also had the hen wiggle at the wrong time, and get food coloring on her feathers, and then it rubbed onto several eggs in the nest (it was something like 3 eggs with the same color on them, and one was a color the hen herself could never lay.)
I wish there were much easier ways to find out which hen layed what without having to watch them lay every time.
 
You could make a trap box, so the hen gets caught inside the nesting box and you see who laid what when you let them out. There were some examples on this site for how to build. It's just a door that closes behind the hen when she goes in. I tried to make some and it can be tricky to get the size right so it closes behind the hen and not in front haha.

If you are worried about some bacteria, maybe it is worth getting a dead chick or two to a vet for a necropsy, assuming you are able to. That is really the only way to rule out disease. But I would also try changing the feed first and cleaning any bacteria off the outside of the eggs as others have advised.
 
I wish there were much easier ways to find out which hen layed what without having to watch them lay every time.
Depending on how many hens and what color eggs, sometimes it works to divide them into several pens. If each pen has one hen that lays white, one that lays brown, and one that lays blue, it is easy to tell who laid which egg.

Of course that does not work when someone has a flock with one rooster and a group of same-breed hens to raise purebred chicks or for most kinds of breeding projects, but it is sometimes worth considering if someone needs to track down a particular problem (which hen is laying eggs that don't hatch, or eggs that have soft shells, or frequently have double yolks, or anything of the sort.)
 

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