Long story short, my ghost sim had ghost babies with non-playable females around town (doing a "populating the town with ghosts" kind of challenge) and in one particular family the house got so crowded I decided to split up the household to make it easier for the NPC's to raise the kids. Well, when I went to Edit town and was trying to split the household, I could only see 8 of the sims (I had used a mod to enable larger households). I thought it was nothing, moved most of them out and all was great, didn't really check on them after that. However, now a bunch of my ghost's kids are aging up - but I still have a ton of baby ghosts in my family tree who are not aging! (Some ghost kids that I can still find are currently toddlers) I figured these may have somehow disappeared from the household when I tried to split it or something because I can't find them around town, and obviously since they're babies I can't call them and since they're ghosts they only show up in the family tree and not the relationship panel. Can the babies be lost, and if so how do I get them back? It would suck to have to make all those ghost babies again because this challenge takes time :/

EDIT: If it's relevant, the mods I have are Woohooer, StoryProgression, Overwatch, ErrorTrap, Mastercontroller, Decensor (all Nraas, obviously) and some kind of mod from MTS which allows vampires to drain sims to death.

It's an old issue, I guess, that you are encountering with inactive ghost babies and toddlers. Everytime all adults leave the house active families receive a babysitter, while for inactives the infant/toddler is temporarily removed from the game and then readded once at least one adult or teenager returns. During this removal, also called hibernation, the inventories of these kids are destroyed and for ghosts this can be fatal. The game considers them as dead Sims and once their tombstone is gone the Sim will not return.
If this is the case these Sims can often be found with MasterController under Type of Sim/Local Minisims. If they are there then it is impossible to get them back, becaus everything except their thumbnail, family tree and traits data are deleted. If they are not there but can be found under other categories then there's a chance to retreive them with MasterController.
To prevent this from happening in the future you'll either need AwesomeMod (option in the config file is NoBabyDisintegration) or NRaas GoHere (options are under Caregivers/Allow Babies/Toddlers To Be Home Alone)

Thank you so much! I will install one of the suggested mods and try it out Will write in this thread if I got it to work after playing a while with it!

---------- UPDATE ----------
I installed the mod NRaas GoHere, and so far all my new ghost babies seem to be doing well and there are finally some ghost children in school THANKS for the help!