He was now fully recovered and is back home with his parents, Kerry, 29, and Mike, 36, and brothers Bryce, 6, and Logan, 6months, in Shelton Lock, South Derbyshire.
Kerry, who runs an art business, said: "He was clearly suffering and his oxygen levels had plummeted when the consultant asked us to make the decision to switch off his life support machine on Good Friday.
"It seemed like a miracle he had survived that long, his CT scans from January when his lungs first collapsed showed he shouldn't have lived through that.
"Mike and I were just thinking of his brothers, thinking whether we were being selfish hanging on to him when he must be suffering so much.
"He's so close to his brothers it was such a hard decision, but the doctors said his organs were failing and there was nothing they could do.
"His temperature was fluctuating through the night and his heart rate was at 200. We were just waiting for him to enter cardiac arrest - as awful as that sounds.
"So we baptised him and said our final goodbyes and at 8am on the Saturday they turned his muscle sedatives off in preparation for the ventilator to be switched off.
"But when they did that suddenly he started struggling in his bed. We thought he was brain dead from oxygen starvation, so he shouldn't have been moving.
"Then the consultant rushed in and said his blood tests showed his organs weren't failing.
"We were trying not to be hopeful, but we just sat by him and hoped and over the weekend he got stronger and stronger.
"We had told Bryce that Dylan wasn't coming back, so when we explained that he had got better Dylan said: 'Oh, so he's like Jesus then.'
"I said, 'you're not wrong'. He had just risen from the dead."
Dylan's lungs collapsed last Christmas Day and he was rushed to the Queen's Medical Centre in Nottingham.
A CT scan revealed cysts on Dylan's lungs had burst and were starving his organs of oxygen, but medics were baffled as to what had caused it.
He made a recovery and was discharged on January 7, but five days later his right lung collapsed.
His chest was drained and he was discharged on February 1, but a week later he collapsed at nursery again and had to be given life-saving CPR.
Kerry said: "It took me three attempts to call for an ambulance, as the first two times they didn't even send anyone out.
"Luckily Caroline Blake, who works at the nursery, managed to keep him going with CPR until the ambulance finally arrived 45 minutes later.
"They found cysts on his lungs that had caused them to collapse and after ventilating him for 48 hours he was stabilised.
"By this time some results from earlier had come back which showed he had Pulmonary Langerhans Cell Histiocytosis.
"There's a one-in-125 million chance of a 3-year-old having that in their lungs - there are only two other cases of it in the UK.
"No one still quite knows why it manifests itself as cysts so doctors didn't know how to treat it. His lungs were 80 per cent covered in these blisters."
He was kept in the intensive care unit at Queen's Medical Centre, but developed an infection on March 18 and his body temperature soared to 40C.
As his oxygen saturation levels plummeted to 70 per cent - 22 per cent lower than normal - medics told Mike and Kerry to say their final goodbyes on April 3.
But when his muscle sedatives were stopped Dylan began kicking in his bed, which showed his brain was still functioning.
So doctors increased the sedation and Dylan's oxygen saturation levels began to increase to a healthy level.
Kerry said: "It really is a miracle that he survived with no real lasting damage from that oxygen saturation.
"He was discharged on April 4 and his last chest drain was on April 20. He's doing so well now, he's running around like normal at home.
"It's just a case of wait and see. The body has to either adapt to these cysts or they will just go away for him to be okay - but the signs are good."
Mike, and assistant restaurant manager, said: "It's incredible, we monitor his oxygen levels all the time and he's actually functioning better than normal.
"At night when he should be at around 90 and 95 per cent he's on 98 per cent.
"We think maybe because he was functioning off 20 per cent lung capacity, now he's got about 80 per cent his body doesn't know what to do with it.
"We just felt so awful when we had to say our goodbyes. And even when he recovered it was mixed feelings - I felt guilty about agreeing to turn off the machine.
"When the doctor came rushing in with his blood test I just looked at Kerry straight away and this wave of hope came flowing back.
"We're just wary of infections now with winter approaching, but it's incredible the recovery he's made."
