Did Upper-class in Europe during the medieval to the modern era have there children learning the the lingua franca of the time (whether Latin, French.. etc) and would not teach them the native language where there from until later or never at all?

The "lingua franca" among men of culture up until the 18th century was Latin, that is why the most important treatises were written in that language, like "De revolutionibus orbium cœlestium", "Principia mathematica", "Sidereus nuncius", "De humani corporis fabrica", "Atlas, sive Cosmographicae meditationes", or "Systema naturae".

That being said, we come to your question. Did anyone from the upper classes educate his children to have Latin as his primary language? Well, there is at least one such documented case, and it is rather famous: Michel de Montaigne.

His parents wanted to raise him to have Latin as his first language, and so they did. They were not only people of culture, but also great enthusiasts of classical antiquity. When the child was present, they would only speak Latin, they would speak Latin to the child, hired servants who knew Latin and who were instructed to always speak that language in presence of young Michel.

C'était une règle inviolable que ni mon père ni ma mère ni valet ni chambrière n'employassent, quand ils parlaient en ma compagnie, autre chose que des mots latins, autant que chacun en avait appris pour baragouiner avec moi

Translation: "It was an inviolable rule that neither my father, nor my mother, or any valet or maid, would speak in my company anything other than Latin, for every one had learnt it in order to chat with me"

This, of course, resulted in Montaigne having Latin as his first language, which they considered a success. However, when time came for young Michel to attend school, he found himself unable to communicate with the rest of the kids, and he communicated with difficulty with the teacher as the kid spoke better Latin than the instructor. Montaigne tells this quite eloquently in his memoirs:

j'avais plus de six ans que je ne comprenais pas encore plus de français ou de périgourdin que d'arabe

Translation: "I was over six years old, and I did not understand yet French or Perigordian more than Arab."

This case is rather famous, as Montaigne would become one of the most prominent figures in the history of French literature, despite French being a second language to him. Given the relatively old school manner in which he writes, Montaigne is known in France as "the last of the classics or the first of the moderns".