don’t really have space for another run to separate Calamity (and wouldn’t want to keep her on her own anyway).
Separating her for a few days might let you become more familiar with what shape & color her eggs are. That might be enough to let you recognize them later.
Beyond that, everything I can think of has some obvious disadvantages.
If you did have room for another run, you could consider getting her one or two companions that lay obviously different eggs (like green, blue, or white, if she lays brown.) Then it would be obvious which eggs from that pen were hers, but she would not have to live alone. But if you don't have room for another run, that clearly will not work.
Some people have talked about putting food coloring or lipstick on a hen's vent at night, to mark the egg she lays the next day. You could test that idea with her in a separate pen for a few days, so you can make sure her eggs really do get marked. Having to re-mark every night would be an obvious disadvantage of this idea.
You could put her in a separate cage or pen each day, then let her out after she lays her egg. Or let her out when all the others have laid, because then you know that any remaining egg must be hers. That avoids penning her ALL the time, but takes a lot of your time each day.
I don’t see who is laying. I have a rough idea, but can’t be completely sure. We don’t want to have to throw away all the eggs we get from now on
If you can recognize half the eggs as not-hers, you could comfortably eat them, which would at least help. That might be as good as you can get in this case. If you get any more hens while she is alive, you could make an effort to get ones that lay visibly different eggs. That way you could at least recognize the new ones.
the vet has just informed me that we now can’t eat any eggs that she lays - ever!
I would definitely ask about what medicines were used and do some research on that. You might decide that the vet is being overly-conservative, and that some period of time is long enough. You could certainly re-check the matter every now and then, in case new research or new guidelines say something different. If you sell eggs, you might have to follow specific rules that don't apply to eggs for personal use.
I know that long-term contraceptives are sometimes used for hens with laying issues. I wonder if that would be helpful in the case of this hen, just to avoid the issues of recognizing her eggs?
And at risk of sounding hard-hearted, you might consider how important it is to you to continue keeping this hen as a pet, and what you are willing to do to make that happen. Since you have already taken the hen to the vet, and are currently asking for advice about identifying eggs, I gather that you are willing to do quite a bit to continue keeping her. I'm not saying you need to change anything, just suggesting that you make sure your actions line up with your own priorities.
