She could have stepped on something long ago, it broke off in her and healed over, leaving the foreign body in her. Or a piece of bone broke off, someone stepped on the foot broke a bone fragment off, foot healed but broken, and not getting nutrients so just dead crap bone, still in her causing issues. Now it finally worked it's way to the surface, you pulled it out, and now she can truly heal because the thing causing the infection is finally removed.
A lot of stuff like that will not show up on X rays, they are not miracle rays and a lot of things, just won't show on them. Ultrasound may reveal a lot more than x rays but each incidence is unique as to what will work and what wont.
I bet she gets better now and rooting for her. I love stories like this where someone sticks with a sick animal and brings it back to health. I used to raise bearded dragons, and for that, i ... inherited some rescues from time to time, horribly treated, broken backs, the works, so yah im very familiar with special needs pets, feeding by spoon or syringe, giving them shots daily etc etc. Sometimes if you let the pharmacist know what you are doing, they can give you a break on stuff you need to buy etc.
I needed small / short needles for subcutaneous injections. They typically balk when you go in and say I need syringes and needles, but when I brought the little guy and showed the pharmacist what it was for he made sure i always had everything i ever needed. You probably can't bring a duck in but a picture or so might help with getting supplies, better prices maybe? I honestly don't know, just a thought, it worked for me at one time,maybe can for you too.
Aaron