I've been looking through the Json save editor like you said. I have two slaves showing they're pregnant in game, yet in the save file it does not say they are after "is_preg." It says false not true. I don't know if that has anything to do with it.
Viewing post in Aric's Expansion Rebred
Slaves impregnated in vanilla gameplay will have a baby ID in the "baby" field but will have "is_preg" still set to false. Slaves impregnated in this mod will have at least one baby ID in the "unborn_baby" field and the "is_preg" entry set to true. However, if the slave was added during vanilla gameplay but not expanded to have the addition data for the mod, then the "is_preg" entry will be missing, which is your primary problem.