The pair finished as runners up on the series earlier this year, but Simon had told the pair they should go their separate ways in their original audition.
However 17-year-old Charlotte revealed this week: “Simon apologised to me for what he said to me in our first audition.
“He said, ‘It’s really nice to see you even though I was so mean to you before. You’ve improved so much since the first audition and I love you as a duo now.’”
Jonathan added: “He was so positive about the album and said he loved the tracks and it was going to be a big success.”
Meanwhile, Jonathan has been shedding the pounds ahead of the launch of the pair's debut album this month.
He said: “I’ve lost just under a stone, which is quite exciting.
“I’d like to look like myself but thinner. I just want to be healthier.”
Speaking to The Sun, a source added: “Jonathan is losing so much weight he is having to be fitted out new suits for the album launch.”
Jonathan and Charlotte's debut album Together is out on September 24.