Having a dedicated hatcher is the proper way. Or, some incubators have dedicated hatching trays. Same same. I do not "mix" eggs from different pens for the very concerns you have @ejcrist .
It is very simple if you hatch dedicated batches. Toe punching or web snipping with cuticle scissors is pretty much fool proof for identification. Do a google search on toe punching and you'll be able to see that you can make up to 16 separate ID's by punching or cutting out different combinations of the four web areas that each chick has.
I covered all this with some extensive teaching posts about two month ago, if you look back, you'll find them.
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