Do get a second opinion so you can understand how to help your mom. Perhaps she needs a fundoplication surgery to keep the acid in her stomach. Perhaps it's a temporary problem that will subside with healing. I have no experience with this, so can't really help you, other than offer support!
See another doc and get some clarification. It's common to develop hoarseness with reflux, but I don't think it's common to bypass surgery.
I did a little searching around, and found some information for you. Bypass surgery generally takes care of reflux, but in your mom's case, it hasn't. There is a version of fundoplication called the Belsey Mark IV, and it sounds like it's an option for those who've had bypass surgery and continue to have severe reflux that doesn't respond to medication and antacids.
Here's a link to a medical abstract that provides some information. From what I can figure out, the Belsey Mark IV isn't all that effective for the general population, but that it is sufficient as a barrier after bypass surgery. Check out te article and see if it helps clear things up a bit.
Nissen Fundoplication 2/09
"Whatever you fight, you strengthen, and what you resist, persists.”
“Worry pretends to be necessary but serves no useful purpose”
“Accept - then act. Whatever the present moment contains, accept it as if you had chosen it. Always work with it, not against it.”