Hi Tsep,
Your case is quite complicated to me. I am not a migration agent but as far as I know, if you have a newborn while in 489 you must notify the DIBP for your baby to have the same visa as yours. Then that's the only time you can lodge your 887 and your newborn can be included on the application. In 887 visa website it states "Family members must be included in your application when it is lodged; they cannot be added after lodgement.", you can only add newborn if she was born after 887 lodgement . But in your case your newborn was born before 887 lodgement. I don't know or heard anybody that did the same thing as you did but I hope it will works for you. Goodluck..
Cheers mate...