Complex sentence: Indigenous languages were studied mainly by the religious orders during the first centuries, and became official languages in the so-called Republic of Indians, only to be outlawed and ignored after independence by the prevailing Spanish-speaking creoles.
Split into simpler sentences: Indigenous languages were studied mainly by the religious orders during the first centuries. They became official languages in the so-called Republic of Indians to be outlawed and ignored after independence by the prevailing Spanish-speaking creoles.