It's an interesting question, but she would have had to get pregnant rather quickly as, by accounts, she began her affair with Culpepper early in 1541 and KH and Henry were married in July 1540.  In which case, if she were pregnant, she wouldn't have been having an affair with Culpepper in early 1541 because sex during pregnancy was viewed as somewhat dangerous at the time.  

If she had gotten pregnant by Culpepper in early 1541 we know she would have been safe at least until the child was born.  No way would Henry have executed the woman who might have been carrying his child.  If the child had turned out to be a boy, I don't think that anything in the world could have swayed Henry's opinion of the boy's paternity.  Henry, though, viewed girls as more expendable and might have been more easily persuaded of another princess's illegitimacy.

I do think that by this point that Tudor law did make it an act of treason for a queen to commit adultery–probably for this very reason.  If a queen was found to be involved in adultery then this would automatically call the paternity of her children into question and, thus, the rightful succession of the throne.  So little was understood about pregnancy and reproduction, and doctors certainly lacked the knowledge to put two and two together and figure out paternity based on menstrual cycles.  If the child had looked enough like Henry, it would have been easy to convince Henry that the child was his.

Would any of this have mattered to Henry if he truly desired to get rid of KH?  I doubt it.  He probably would have just had someone create charges of witchcraft and gotten rid of her that way.  This would have allowed him to maintain the legitimacy of his bloodline and eliminate Katherine.

MegC said:

I do think that by this point that Tudor law did make it an act of treason for a queen to commit adultery

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It had, in fact, been the law since the Treason Act of 1351. It decreed the man would be hanged, drawn and quartered. The woman was to be burned at the stake.

As brutal as it sounds, Henry could have killed Kathryn and still kept the son as his heir.

What a question! I've often thought something similar. Personally I think if Katherine had given birth to a son then definitely under any circumstances the Henry would have spared Katherine and accepted the son totally as his own even if the child's mother was under suspicion because a son to Henry was absolutely everything. We all know Henry bent the rules for himself so any charges against her he would make sure that they were bent to suit what he wanted to believe. Henry was without doubt a law unto himself.

Did Culpeper have red hair?  Otherwise there would be big trouble if that baby came out with dark hair.

I don't see a scenario where Henry would not have found out about Katherine and Culpeper. Someone would have known and he would have been told. So, I start from that point.

If Henry found out about the affair, and then found out she was pregnant, Katherine's execution would have been postponed until the baby was born. Katherine would not have been safe, whether she had a boy or a girl.  Culpeper would have been executed immediately.

IMO, if there was any doubt that the child was his, Henry would not claim it.  He was no longer desperate for a son.  I could be way off base here, but I cannot imagine Henry accepting another man's child as his own.  If this child were a boy, he would still be the spare.  Henry already had his heir. 

 It was whispered at court that Henry was the father of Mary Boleyn's child/children.  He never claimed them as his, IMO, because Mary was married, and there would always be doubts as to whether Carey was the father or not. I can't see Henry living with that kind of doubt about a child.

Either way, Katherine and Culpeper would lose their heads. 

That's an interesting thought, E. On one hand, Henry was of course desperate for another son. On the other hand, would he really take the chance that the child (and possible heir to England) was Thomas Culpeper's? I believe that Henry would ponder it and attempt to convince himself the charges could not be accurate; but with the Howards so hated, who wouldn't jump at the chance to prove the affair and get rid of both Katherine and her son? Plus, Henry had a strong sense of manly pride, and he would not want people to whisper that his 'son' the Duke of York was really Culpeper's (imagine the rumors: “He doesn't have the Tudor hair! And look, Thomas Culpeper's nose for sure…”). Unless Cranmer and Wriothesley, not wanting to risk the King's displeasure, buried everything under the rug…