The father of a 2-year-old girl with medical issues who was asked to leave a Panera Bread restaurant because the noise of her shoes was bothering a customer says the family was "shocked" by the restaurant's actions.

"The employee and the manager knew what we'd been going through with Emma because she and my wife go there so frequently, Stephen Duke told GoodMorningAmerica.com. "They knew why she had the shoes so that's the thing that shocked us the most."

Two-year-old Emma Duke was at a Panera Bread in Savannah, Ga., with her mom, Catherine Duke, on Jan. 2 when an employee told Duke that she needed to either take off Emma's shoes or leave the restaurant.

Emma suffers from a still-undiagnosed illness that has led to developmental delays, including the inability to walk.

"She just started to try to walk at 23 months, which is very late, so the orthopedist recommended special shoes to her for better ankle support," said Stephen Duke. "The shoes squeak as an incentive when she walks heel to toe, so she'll hear it and know that she's walking properly."

The squeaking noise, according to the Panera employee, bothered a customer, prompting the request that made Catherine leave the restaurant in tears.

"I think she had been working there for a number of months," Duke said of the employee, who has not been identified.

Catherine Duke later followed up with Panera's corporate headquarters to complain about the treatment, prompting an in-person apology from officials with the Missouri-based restaurant chain.

"On Saturday, Catherine and Emma met at the restaurant with corporate staff, the employee and the franchise manager," said Duke, a firefighter who was on duty at the time. "They apologized and said that is not something Panera does and that they want to be a welcoming store."

The officials also pledged to hold a fundraiser for the Dukes in the coming weeks in which 50 percent of the restaurant's proceeds on a given night will be given to the family to help offset Emma's medical bills.

"We're not expecting a handout by any means but we do appreciate the fundraiser because Emma's bills for all the specialists and treatments are enormous," Duke said.

Duke said that his wife, a stay-at-home mom, frequented the Panera as a low-cost way on their tight budget to get out of the house with the kids, both Emma and Duke's other daughter, three-year-old Ana.

While Duke says he "probably" won't return to the restaurant, his wife, Catherine, probably will.

"She was friends with some of the people who work there and I think she'll probably go back, although I don't know if as frequently," he said.

When reached by GoodMorningAmerica.com, Panera Bread issued a statement saying they believe the issue has been resolved.

"As you would expect, Panera Bread does not tolerate discrimination of any kind. The last thing we would want to do is make anyone feel unwelcome. Consistent with this system-wide policy, our franchisee met personally with Mrs. Duke to directly hear and address the concerns she has raised. We understand from our franchisee that Mrs. Duke has been assured that she and her family are always welcome at Panera and her concerns have been addressed."