The company that took the photo, Lifetouch, quickly apologised on its Facebook page, saying the photographer made an "unintentional" mistake.
"We worked directly with the family and school to retake the class photo and the new portrait was delivered yesterday," Lifetouch said on Wednesday.
The new photo shows Miles, out of his wheelchair, sitting with his classmates in the front row, the same toothy grin lighting up his face.
After seeing the new portrait, Miles father Don Ambridge said "the world’s been put back as it should be".
Mr Ambridge and Miles’ mother Anne Belanger were shocked and upset by the original photo and refused to let their son see it to avoid hurting him.
But Mr Ambridge, who attended the reshoot last week, said he did not think the school or photographer were being intentionally malicious.
Mr Ambridge told NBC’s Today Show that Miles chose to sit outside his wheelchair for reshoot.
"That’s his decision to make, not others," he said.
"When we get home from school the first thing he wants to do is go hang out on the couch and maybe play some Wii, maybe read a book – he wants to take a break from the chair."
The family hopes the incident will shed light on discrimination
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