I don't know what it is about Welsh harlequin, but drakes seem to want to go after them and they get picked on more than others. I have had it in my flock and read about it in others. Eventually the drake and her should work things out. But until they do, it will not be fun for her at all. I am not sure how true it is with ducks compared to other animals, but often with pecking order, if you stop it from being established, they have to start establishing it all over again. But I totally get needing to protect your older gal. You might want to have them share a fence line. That way they can squabble at the fence line with no consequences.
Depending on how long they are separated from the flock, can affect the flock. I was treating my pekin for bumblefoot for a couple months. Her pen was in the area with the other ducks, but she is no longer the top female.
