eBay can't auto deduct any money I don't think.. eBay operates as a separate entity from PayPal so PayPal can't do this even if money is owed to eBay.
If your mom has never sold on eBay, then she should have never had to pay fees, let alone enter her info. Is it in there for some other reason?
If not then I'm not sure how they will auto-deduct anything.
I would suggest trying live chat again and seeing if it works. It has always worked for me. Can't guarantee they will give you good news but if you have the other email from them stating that they would reverse all charges, then you should be safe for sure.
Don't let them go back on their word on this one. I think it should be a simple miscommunication and if given the opportunity to explain the situation, you should be fine I hope.