Bad news, went out to the pen to find a shell-less egg again today

Makes me think the problem is not solved after all.
So, by process of elimination, I have figured that neither of my 2 drakes laid that egg, neither has the youngling, my Khaki Campbell seems to have returned to laying in her own (wierd) preferred spot, under a ramp, and the good eggs I'm getting look like Pekin sized. So that leaves the two Rouens, one of which had the "funny" looking vent back of the beginning. I suppose it is possible that the Lady with the issue could be the Jumbo Pekin that hatched in Spring, altho I'm not so sure of that since i did surprise her in the act of laying a few weeks back and that egg was perfect. So I'm down to 3 likely candidates. Now what!? How do I identify which duck it is?
Now last year I visited a working historical farm and I learned how the workers were able to identify which ram sired which lamb in a flock of many. I think the rams chests and abdomens were dusted with different colored chalk. After mating, dad would leave a chalk mark on the ewe, clearly demonstrating who had mated. So my question is, is there a technique similar to this that I can use with my ducks and their egg laying? Non invasive, hopefully!
And Amiga, I still have the liquid calcium, I haven't given it yet because a) I wasn't sure of the best method of delivery or proportions, and b) if I need to isolate each suck to avoid dosing my drakes or my healthy flock members.
Well. Experts, thank you for your input! Have a beautiful day.