This is going to get a little confusing with all the begetting, but I want you to have all the info I do to help me figure this out. Names have been simplified to help out all concerned. Children are named oldest first youngest last. It takes place in Byzantium with all DLC loaded.
Emperor John beget Molly and Susan, Molly beget Adam and Steven, Adam beget Elise and Isaac.
John died Molly inherited Empire (Susan was heir until Molly had kids).
Molly died Adam inherited Empire (Steven was heir until Adam had kids)
I married Susan. I murdered Steven, Elise, and Isaac. They had no children. Susan is now heir again. We have 1 son (my heir). If Susan dies prior to the death of the current emperor and he has no more legitimate children. Will my son become heir?
I think the answer is yes, but I really don't want to bugger up my ironman game by assuming that he will and since I don't really understand the "Born in the Purple" trait I thought I should ask.
Best Answer
Why not use the line of succession tooltip you get when you hover over the title of the Byzantine Empire? That will tell you if your son is next in the line for the succession after your wife. Here's how you'd do it:
Click on the main province of the title in question (for your case, it would probably be Constantinople, because that's normally where the Byzantine Empire is based).
Hover over the shield of the title in question, this will result in a list appearing showing the next 3 people in line to inherit the title. You're wife is next in line, so she should be ranked #1. If your son is going to be next in line to inherit if she dies before attaining Empress-ship, he'll be ranked #2 right now.
Assuming the succession laws are the same as the default Byzantine Empire, then we can use this excerpt from the ck2 wiki to figure it out by hand:
Due to agnatic-cognatic succession, rule 1 means that the male children will take precedent. Rule 2 further specifies that it will be the oldest male child, or Isaac. He's dead, so when we reach rule 3, we go to rule 4, because Isaac had no children. So we go back up to Adam again. We repeat the process with Elise, to the same end, and then, now that Adam has been established as having no direct descendants, we move up to Adam's mother, Molly. Molly, of course, only had Adam, so we move up to John. Besides Molly, John only had your wife, so we move down to her. She is dead, so we move to her children, which is your son. He is alive, so he gets the title. So, as far as I can tell, Yes, your son will inherit if your wife dies before becoming Empress.