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:
The heir to a ruler's title with primogeniture succession is determined through several steps, ranked from more to less important. Through this whole process, all people are assumed alive, even those who are dead.
The eligible children of the ruler are divided into man/woman categories if gender laws apply. These categories are ranked according to these laws.
The eligible children of the ruler are then ranked within these categories according to their age.
The highest ranked child inherits the title. If this character happens to be dead, he is considered to have died just after his inheritance and steps steps 1-3 are repeated to determine his/her heir.
If there are no eligible heirs to be found among a dead character's descendants, this character is disqualified from succession and we move up to his/her father as the heir. Again, if this person happens to be dead, he is considered to have died just recently and we start the process again until an eligible heir has been found.
Under agnatic-cognatic succession: if a woman is found to be an heir but she has son(s), she will be ranked after her son(s).
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.