Complex sentence: Therefore, the champions Santa Cruz (Copa do Nordeste) and Paysandu (Copa Verde) lost their Copa Sudamericana berths but they were qualified to the 2017 Copa do Brasil Round of 16.
Split into simpler sentences: Therefore, the champions Santa Cruz (Copa do Nordeste) and Paysandu (Copa Verde) lost their Copa Sudamericana berths. Finally, they were qualified to the 2017 Copa do Brasil Round of 16.