This happens during my story 'Meetup' and is one of the reasons Lois is at Wayne Manor while Conner happens to be there.
As usual I own nothing but my own ideas.
Clark sat across the kitchen table in the family farmhouse fidgeting nervously. If the supervillains of the world could see the mighty Superman squirming in front of his Ma and Pa all his credibility would be gone.
"Clark, we asked you come home because there's something we wanted to talk to you about." Jonathan began. Clark's eyes jumped to Jonathan. He felt just like he had in high school when he had gone out with Pete and some of the other guys drinking underage. He couldn't get drunk but the rest had so they had gotten caught.
"Is something wrong, Pa?" Clark tried to keep his voice level, he really did.
Martha sighed and slid a newspaper clipping across the table. The photo attached to it was an action shot of Robin and Superboy. The photographer must have been very close and as good at his job as Jimmy Olsen. The photo was quite clear and showed an excellent shot of Superman's crest on the teen's chest.
"Is there something you wanted to tell us?"
"It's not what you think." He stammered out.
"Clark." Martha's hand closed over Clark's. "You know you can tell us anything. Sometimes accidents happen but that you hid this boy from us all these years –"
"No! He's not my son!" Clark shoved up from the table and across the room to stare out the window. "They stole my DNA. He's a clone, created in a lab. He's not mine."
Silence reigned in the kitchen. Clark stood staring out the window waiting for his parents' horrified responses.
"Start talking." Came quietly from Jonathan.
Clark turned, leaning against the kitchen counter, and began telling the story. Of the boys disobeying orders and finding CADMUS, freeing Superboy. That the four of them formed a team with Miss Martian and other protégés joined, working under the direction of Batman. The decision he had made to only have contact with the boy when League or Team business demanded it. That Batman had taken over his care and training. His voice was quiet by the end and he looked down at the floor. "I'm sorry this happened but I had no control over it. I'll tell Bruce Superboy has to be more discrete; that he upsets you."
Jonathan and Martha exchanged a glance. Martha spoke. "You think this boy upsets us?"
"He doesn't?" Clark looked up at his parents.
"No. What upsets us is that we had to find out about Superboy from a newspaper," Jonathan frowned at Clark.
"Superboy, well this is silly, I'm not going to call him 'Superboy'. What is his name?" Martha smiled at Clark, encouragingly.
"What?" Clark looked confused.
"Superboy's name." Martha was still smiling. "What's his real name? And I suppose he'll need an El one as well."
"His name? He didn't have a real one. They just called him 'The Superboy' at CADMUS." Clark remembered something. "Although, when Bruce was trying to get me interested in him he mentioned something about enrolling him in school so they must have had to give him an actual name."
"They called him 'The Superboy'? Like he was a thing?" Martha was outraged. "And you don't even know if Bruce has given him a name since then? Or what it is if he has one?"
"No Ma'am." Clark replied weakly.
"Clark, we raised you better than this." Jonathan sighed. "When we found you in that field we never questioned that you were ours. You just were. Now you're telling us that this boy, this boy who shares your DNA, isn't good enough to be part of this family? Because someone made the decision for you and him about how he came to be? You have a right to mad about that. I'm mad too but that boy isn't at fault. What he is though, what he should be, is a member of this family."
"As much as I think that Bruce does a marvelous job with Dick I think that he isn't equipped to train a Kryptonian, especially a teenage one." Martha rose and walked over to Clark. "Now don't you think you would be the better one to teach that boy how to handle his powers?"
"Marvelous job?" Clark snorted. "Given the company he lets Dick keep I don't know that I think he does such a great job. Apparently, he's letting Selina Kyle supervise Superboy too."
"Clark Joseph Kent don't you sass me." Martha stared at the Man of Steel who towered over her.
"Sorry Ma." He mumbled ducking his head.
"We don't judge people on their pasts. Dick tells me Selina has cleaned up her life. I know that she runs all those charities and I also know that she works with Batman now, even helps the Justice League from time to time." Martha folded her arms. "You left responsibility for that boy with Bruce. You don't get to have an opinion on what he does with him. You want a say, you step up. Am I clear?"
"Yes Ma." Clark lifted his head again and looked from his mother to his father who nodded at him. "I'll, ah, get it figured out."
Oh yeah, it was best that the supervillains hadn't seen this. Or the Justice League. Rao help him if Ollie had seen it. The man probably wouldn't stop laughing for a week. After all, he had tried to warn him.