One of the reason the brazilian emperor D.Pedro I declared independence from Portugal, was because he knew that the demands of the portuguese at the time made the independence inevitable, since they wanted the entire royal family to go back to Portugal, with them also wanting to take away the newly gained status the colony had attained since the stay of the royal family there. He realized also that it would be more advantageous and secure if he himself declared independence, rather than allow the country to be fragmented in many little small republics, marked by dictators and civil war, like the rest of South America.

But after he made that decision, the troops loyal to Portugal had to be fought and brought under control, which helped consolidate the newly formed nation and showed his leadership skills. However, the Cisplatine War was one rebellion, aided by the Argentinians, where Brazil lost, with Uruguay separating itself from the rest of the country, becoming a new nation. This wasn´t the last rebellion or war that Brazil fought either, since after that there were many others, varying in scale and impact, they were: "Sabinada", "Cabanagem", "Farroupilha" Revolution, Platine War, Uruguayan War, Paraguayan War, "Praiera" Revolution, and the Federalist Revolution.

Note that not all of those had a separatist intention, but all of them represented a danger to Brazilian territorial integrity. If Brazil is one big country, instead of many little ones, is because of the hard work and expertise of military figures like Duke of Caxias, and politicians like Diogo Feijó, Bernardo Pereira de Vasconcellos, José Bonifácio, and many others. Basically, Brazil had to fought many times to maintain it´s vast territory.

Sources: História dos Fundadores do Império- Octavio Tarquinio de Souza. História de D.Pedro II- Pedro Calmon. A Vida e Época do Visconde do Rio Branco- Barão do Rio Branco Caxias- Affonso de Carvalho.