Yeah this is a known thing. You have to let whatever sim ages the baby up into a toddler go all the way through the "First Steps" action with the toddler before going into CAS via MCCommand Center or it will reset time (I assume because the birthday isn't fully complete yet so the game hasn't fully registered it yet). I believe with MCCommand Center you can adjust their family relationship but I'm not sure the steps that are needed to take to do it. There's a Help Thread for the Mod
HERE which is probably the best place to ask about it.