Green card holder filed relevant document and issued payment for being able to stay outside US for more than 6 months. However, due to difference in the amount(revised for some reason) payment was returned. Now it seems the only way to apply is in person. But she s already left and it is already 6 months.
What is she to do?

Come in as soon as possible, with evidence of ties to the US as well as evidence of the attempted filing of the I-131.

She is not in good health and might not be able to fly in soon. Can she not use her application number to do anything about it. As it is she s already crossed the 6 month period she was told about. The confirmation of her stay was to come to her India address. Instead they returned her payment to her US address

Come in as soon as possible, with evidence of the emergency medical treatment. Stop concerning yourself about the returned I-131, the CIS and the CBP do not care, nor will they admit any error. Show that you attempted to file it.