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This could be a long, drawn out experiment, but worth it if you want to locate the source. This is what I'd do:
First, you'd need to separate the hens for close to one month to make a clean "control", where they wouldn't retain leftover rooster semen. Then you could separate them into 2 breeder pens. Let the separate pairs breed for 2 weeks (hoping this swap around doesn't mess up the hen's laying cycle). Set all of the eggs and label them clearly. Pen 1 Rooster X/Hen X and Pen 2 Rooster Y/Hen Y. When they hatch, zip tie a color on the X pen chicks and another color on the Y pen chicks.
Take the hens out for another month to make certain the rooster's semen has gone. Then switch the hens into opposite pens. Breed them for two weeks. Pen 1 Rooster X/Hen Y and Pen 2 Rooster Y/Hen X. Set all eggs and label them clearly. Again, when the chicks hatch, put a colored zip tie on the legs of the X rooster Pen 1 and a different color on the legs of the Y rooster Pen 2.
If the first set of eggs yields an "off" chick, you'll know if it came from the X pen or the Y pen. And after the second set, if you have "off" chick, you will be able to narrow it down to a rooster or a hen passing that on.
So if you have off chicks from X/X Pen 1, and the following set have off chicks from X/Y Pen 1, you know it is the rooster throwing "off" chicks.
I haven't had my coffee yet, so if this doesn't make sense, I blame it on a lack of caffeine!!!
OR, you could take one rooster out of the pen...and after 3-4 weeks start keeping track of both hens by putting food coloring in the vents of the hens...Blue for hen X and red for hen Y. Set the eggs. Then after 2 or 3 weeks of that pairing and egg setting, take out that roo. Put roo #2 in with them, wait 3 to 4 weeks to make sure there is no semen from Roo #1 leftover and start another set of eggs. Put food coloring in the vents of the girls (a few drops near the outside and they will suck it up in the vent)...Again Blue for hen X and Red for hen Y. Set those eggs.
This may give you a better leg up on always having fertile eggs (the inbetween test period) if you need them. Make sure you label your eggs clearly from which hen laid which, and from whichever rooster was with them. You could also only do one hen with the vent food coloring method if you are only working with two hens, they would be easy to keep track of.
Anyone else have any suggestions?
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