I'm not entirely sure where to post this, so please let me know if its wrong.
The main family I created had two babies while they weren't the active family and I was able to view one of them, but not the other. Now I can't find her. She shows up on the family tree, but not in the relationships or anywhere else. I've looked in the old house that I moved them from and even the family I was playing when I found out there was one. I checked all of the households. Nothing.

She was probably taken by the social services.
Do you have EA's Story Progression on?

Nope, how do you do that?

If it were social services, surely there'd be a warning that they're about to come steal your babbies? So unless OP missed any notification warning of a visit, she'd have realised?

I was playing another household that was related and saw that there were two more babies. Would it matter if one was still around and the other wasn't?

Are you using EA's vanilla Story Progression? Babies sometimes disappear from inactive families with EA Story Progression on. Also, have you tried resetting the baby?

But the male baby was still there while the female baby wasn't. I'm at a loss.

How do I reset that baby? I've never tried it before.

By Crinrict:

"Inactive babies and toddlers are being taken out of the world when the household they live in does not have the focus. They should get back into the game once you focus on that household or make it active though (although there might be sometime a problem with that, making those gone for good)."

"Babies have the tendendy to die (even if they don't show as dead in the family tree) when inactive so chances are that what's happened. The icon of dead Sims only change into their black/grey variant if the Sims appeared as ghost once. Usually for inactive babies that die that doesn't really happen so they often show as alive although they are in fact dead. Inactive babies should not die in my opinion so this is a bug but it still happens cause they are not protected."

http://answers.ea.com/t5/The-Sims-3...ies/td-p/487542
http://sims3.crinrict.com/en/2011/0...issing-sim.html

To reset a Sim: open the console by pressing shift+control+c, type resetSim Firstname Lastname, hit enter. Story Progression is on by default, so unless you've tinkered with the settings, you've probably got EA story progression on. It's pretty wonky, you'll probably want NRaas Story Progression at some point.

Thanks! I hope I can get it back.

Wasn't able to get it back. My husband reset the hard drive in hopes of helping, but in turn lost my saved games completely! ( I've started over lol.

I've had this same issue when I was using EA progression. Try this mod, it prevents losing sims(babies included).
http://nraas.wikispaces.com/Overwatch
Even if your save is gone, you don't want it to happen again, right?

EA drowned and starved two of my Sim's toddlers at one time, the only way you'll know is if you read the paper. I was so creeped out when this happened .

That's what I hated about EA story progression; The Keatons' baby, Claire Ursine's baby, and a bunch of my CAS families' babies were killed. Luckily, that save game was destroyed and when I started over, I was more careful

She could have been killed. One of my non-active sims was born with Story Progression on (EA's) and they never fed her. She probably died

I'm not sure if this has been resolved and I might be late responding, but do you have NRaas Overwatch installed. That mod recovers stuck sims, missing toddlers etc. during it's nightly clean up. Debug Enabler also has options for resetting and fixing invisible sims. If you do not have these mods, and do not mind using mods, you might want to look into these mods going forward.