It has been so often stated that Maya science was lost largely because of the extermination or driving out of the native priests after the Spanish conquest that it is of special interest to note in the documents of the 1562 proceedings that a large number of these priests were still living and secretly practicing their profession. Only once are local priests named as taking part in human sacrifices at the pueblo of Sotuta, but we find three assisting priests from Yaxcaba and Tixcacaltuya also taking part. At Kanchunup six priests are named, at Mopila five, Yaxaca four, Tibolon four, Usil two, and at Sahcaba only one. All but two at Mopila had Christian names and had evidently been baptized; and one of the Usil priests, Juan Pech, had learned his profession while acting as schoolmaster, an office which he still held.
Pressure by the missionaries no doubt diminished the number of neophytes as time went on; but it now seems probable that the disappearance of Maya religious and scientific lore was very gradual and Maya astronomy in course of time gave way to European astrology, of which we find much in later Books of Chilam Balam. From the 1562 inquiry we learn that the local schoolmasters were frequently present at human sacrifices and reports made by the encomenderos to the king in 1579 still accuse these men of being great idolaters and even keeping idols in the schoolhouse. There can be little doubt that this class continued to carry on the old traditions for a long time and were the men who compiled the so-called Books of Chilam Balam and kept them in circulation.
Religious syncretism was obviously developing in Yucatin as early as 1562 when sacrificial victims were also crucified in the European manner.
Richard E. Greenleaf, “Persistence of Native Values: The Inquisition and the Indians of Colonial Mexico,” The Americas, vol. 50.3 (1994)