After an incredibly annoying and somewhat exhausting research that /u/Georgy_K_Zhukov and I conducted over the last couple of hours, I think it's possible to cut through the confusion: The painting shows not just Maria Theresia's dead children but contains a nod to her grand-child Christina, born in 1762 by Isabella of Parma, wife of Maria Theresia's son Jospeh II.

Maria Theresia had 16 children, five of which died before becoming full adults but only three of which died very early: Maria Elisabeth (1737–1740), her first child, died suddenly at age three of unspecified reasons.

Maria Karolina (1740–1741), her third child, died of severe cramps at age 1.

Maria Karolina (1748–1748), her tenth child, barely lived two hours after it had been born.

While several of her children had nichnames by which they were called – Marie Christine (1742–1798) was called Mimi; Maria Karolina (1752-1814) was called Charlotte – the most likely explanation going by the names Martin von Meytens who painted the picture in 1765 as part of the Habsurg family portraits in the Innsbruck Hofburg is that from bottom to top, it's Elisabeth, Karolina I, then Karolina II and finally Christina, grand daughter of Maria Theresia.

There is no reference to any other stillborn or miscarried children with Maria Theresia and the only child called Christina or Christine survived until adulthood so according to our research with book like Franz Herre: MNaria Theresia, 2004 and Hanne Egghardt: Maria Theresias Kinder is that one.