@Freedom_Fries911
I'm sorry you couldn't find them. Tbh, I may have been thinking about how it worked in TS2 as @jpkarlsen said. It has been a long time since I looked at adoptions so I just may have forgotten how it works in TS4.
As @xochiquetzl_xkvn and @jpkarlsen said, they've probably been culled then. There is a way to get them out of the family tree but it comes with the cost of losing all the main sim's relationships and disconnects him from other family if he has any. He'll have to start all his relationships again.
You could save the main sim to your library and then delete the one in the game and replace him with the copy from the library. The sim will keep all his skills and aspiration progress (I think the library keeps the aspiration progress anyway). You might want to test in a new game just to be sure what happens to the aspirations to see if those get carried over or not. If there is another sim in that household, you could transfer the inventory to that sims so you don't lose the inventory items or the collectibles. Or you can place them all on the floor of the house and put them in the replacement sim's inventory when you put him in the house if you don't have another sim in the household.
If you use MCCC, you can reestablish all his family connections fairly easily so there is a way around that if you can use mods. I've done that with some of my sims although I never tried it with babies. I know it works with toddlers and above. It can be a lot of work so you might decide to live with the 2 portraits rather than go to all the trouble. I only mention this if really bothers you and want those portraits gone. It just depends on what you want to do really.
Hope this helps.