Do you know how long was the soft shell inside her? Broken shells inside can lead to egg yolk peritonitis (EYP) or EYP can lead to soft shell eggs that break when the hen tries to expel it.
How do her poops look? Are you still seeing yellow urates? If you are she is still fighting the infection and/or the yolk has not completely been expelled. How does her vent look? Is it swollen or red or does it look normal? Can you see or feel anything around that area?
My girl did not have a soft crop, but I have read that when things at the end of the digestive system get wonky it can slow everything else down. How does her breath smell? Is her crop emptying overnight? Is it nice and flat in the morning before she has any food or water? A sour smell would indicate sour crop and a crop not emptying overnight means that something in the digestive system isn't working correctly.
I am going to look and see if I can find a thread that talks about dosage and duration for EYP. I will tag this thread when I find it.
I would imagine that the longer the egg yolk was inside the more infection that she will have to fight off. Keep up with the amoxicillin and hopefully she will bounce back.
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Admittedly, I am no expert in this area of chicken care. Perhaps
@Wyorp Rock or
@Eggcessive might have better advice for you and your girl.